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  • Adorkable: The player's partner. Notably, they'll be this way regardless of whether you ask for them to be "cute" or "cool", as this question only determines the species that is pre-selected for you and not their personality, which is always this trope.
  • Base-Breaking Character:
    • The player's partner has become this more and more since the game has been out. Some find their actions in the early game hilarious, while others find them genuinely annoying. Some feel their Character Development in the late game makes up for their early game shenanigans, while others feel like their Character Development was shoddily put together and as such steals the spotlight away from some of the games more interesting underdeveloped characters such as the Expedition Society and the player character themselves. The whole "being the reincarnation of Mew" thing doesn't help matters either. Some found it was handled well and was a great twist, while others found it a massive Ass Pull just to subvert the standard PMD ending.
    • Ampharos. Some like him for his Crouching Moron, Hidden Badass tendencies and see him as a funny yet effective Big Good. Others find his No Sense of Direction shtick to wear thin almost immediately and feel he's a transparent and inferior attempt to emulate Wigglytuff from the Explorers games.
    • A lot of the Expedition Society members are this, thanks to a lot of them feeling underdeveloped in comparison to other characters. Bunnelby, in particular, gets a lot of arguments thanks to contributing practically nothing to the story and for the most part just feels "there" whenever he's actually in a scene in the story. In addition, quite a few love how quirky the society as a whole is, while other find a greater part of them annoying.
  • Best Level Ever: Calm Craggy Area. In a game balanced around having three party members at once, this dungeon gives you seven. It's one of the easiest dungeons in the game, but considering how difficult the road up to it is, nobody's complaining.
  • Broken Base:
    • The return of the hunger mechanic. Some like the idea of it returning, others find it an unnecessary annoyance that forces you to eat up inventory space for food.
    • The Looplets and Emera system, replacing the previous entries' IQ/Team Skill systems. Some find them to be a fun and strategic system since the Emera you get are dependent on the RNG, forcing you to stay on your toes; others feel that since the Emera and their effects always disappear after every dungeon, sticking you back at square one, there's never a sense of long-term progression, making them feel unsatisfying. The Looplets also replace all of the hold items from the previous games, like the scarves, scopes, and so on. Some feel that this is a good change, cutting down on the loads and loads of items that you could find before; others feel that this makes the dungeons feel less interesting to explore, since there's far less unique treasures to hunt for.
    • The Connection Orb system, replacing the randomly-generated missions and the recruitment mechanics. Some find it to be a well-done fix, making it much easier to recruit new Pokemon and get 100% completion; others feel that the finite amount of missions hurts the game's replayability, and feel that since it's so easy to unlock powerful, high-level Pokemon, it doesn't feel as rewarding to recruit them. The system only allows for one of each kind of Pokemon to be recruited (save for some rare exceptions such as Pokemon with gender differences or multiple formes). Some think that this makes it easier to track all the Pokemon you've collected on the way to 100% completion; others feel like this reduces the personalization aspect, making recruiting Pokemon feel less like building a team and more like completing a checklist.
    • The slow speed of leveling up. Some find that this, alongside the Looplets and Emera, makes the game much more in line with the rest of the roguelike genre, since you can't easily grind and become overpowered like in the previous games; others, similar to the Looplets and Emera, feel that the slow leveling speed robs the game of a sense of long-term progression, making the gameplay unsatisfying.
    • The motivation system, wherein certain Pokemon can become "motivated" at the start of the day, tripling the EXP gain by 3 (or 6, if an Unown is motivated). Some feel that this serves as a great way to encourage players to try out all the different Pokemon they've recruited; others feel that this restricts players who prefer to stick with their favorites, since the normal leveling speed is so slow.
    • The overall difficulty spike, especially in regards to Gates to Infinity. In addition to the aforementioned hunger mechanic, removal of the IQ/Team Skill systems, and Anti-Grinding mechanics, dungeons and the enemies in them are much more powerful than before. Longer dungeons tend to be grueling even if your team is at a high level. For example, even using a super effective attack that does 100+ damage on an enemy will almost never faint it outright, and enemy attacks that are at a type disadvantage towards you still do sizable damage. While some players appreciate this level of difficulty, especially after the complaints that GTI was too easy, others are frustrated and feel as though making the game so difficult makes it hard to feel a sense of accomplishment.
    • The early game tends to get a lot of arguments over how it was handled. A lot of people feels it was nothing but pointless Filler just to make the game longer and that you could have easily removed a greater part of it without having much impact on the plot. Others, however, liked how the game played things relatively realistically in comparison to past PMD games, with the player and partner being rather limited when it comes to what they can do and have to do a lot in order to prove themselves capable of taking care of themselves to others. An additional camp feels like it could've been good and very effective for a shift in mood...in a different Pokemon game, and not a subseries that's been established as having a dark and mature story since the first entry. Due to being the fourth entry, and a considerably well-known one due to the popularity and love Explorers got for its writing, everyone already expected it to get dark as it progressed instead of it being a surprise.
    • Outside of Pikachu (admittedly was a main in Yellow), and Riolu, the non traditional starters like Meowth, Vulpix, and Eeveenote  are absent again which is a point of contention. Adding an insult to injury, Riolu isn't a starter in mainline games at all.
  • Contested Sequel: Despite fixing the main points of criticism about Gates to Infinity, some still feel this game manages to be even worse than it thanks to both issues with the story and a much, much heavier emphasis on the Roguelike elements. See Broken Base for a list on the main complaints about it, as well as Nintendo Hard and Difficulty Spike on the main page. However, there are some fans that consider it a Surprisingly Improved Sequel.
  • Continuity Lockout: There is a very large amount of references to previous games in the Mystery Dungeon series, from the many Pokémon that you can connect that are actually characters from previous games, being able to travel to the continents of the other Mystery Dungeon games ala Pokémon Gold and Silver, and the multiple regular plot twists that are played around (most notably the partner being the one to disappear instead of the player in the ending). It's mostly agreed that the game's most impactful elements are not so significant if the player hasn't played the previous entries beforehand.
  • Demonic Spiders:
    • In previous installments of the Pokemon Mystery Dungeon series, Ditto would simply appear as mimics of other Pokemon when you encounter them in a dungeon, making them little different from standard encounters. Come Super Mystery Dungeon, however, Ditto now appear to be perfectly normal items until picked up, whereupon they transform into the unwary adventurer and confuse all of its teammates. Your first encounter with them comes in a dungeon with a guest character who is at least twice your level. If you don't have a way of eliminating a copy of yourself quickly, chances are good that you'll be knocked out by your own teammates' wildly thrown attacks. The cherry on top? They can be any item, and there's no way to detect them beforehand, even with Emera that sense objects and enemies, or by attacking items first.
    • Many enemies have moves that can render you entire unable to do anything. This is especially bad when you're thrown into solo dungeons, or when you have to face multiple enemies like this.
    • Bug- and Flying-type Pokemon often have the Bug Bite and Pluck moves respectively. These moves allow them to eat Oran Berries and Reviver Seeds right out of your inventory, causing them to: 1.) damage you, 2.) destroy your healing items, and 3.) heal themselves so you can't kill them, all at the same time.
  • Difficulty Spike:
    • Choose any dungeon early on that's not from the story mode or the Water Continent, and your sorry kiddy ass will be handed back to you.
    • In terms of the story, Poliwrath River is a major one especially if you chose Fire and/or Water types. Prepare for Luxio dealing insane damage with a Charged Spark and Heliolisk hitting an entire party with Razor Wind. The three Poliwrath (and Poliwag) waiting at the end are no joke either, as they will try to surround one Pokémon and spam Round, which gets stronger as more Pokémon use it.
    • The Submerged Cave is outright cruel, with wild Pokémon being able to use Hydro Pump to hit a whole team in a straight line. The damage can easily cap above 100 HP, while your choices haven't left the double digits yet. Grass-type starters may barely survive one hit (without taking into account that Rain Dance may be in effect), but everyone else...
    • If you chose a fire-type as your player character, the Sand Dune of Spirits is probably going to give you a hard time if not outright kick your butt. There's no avoiding it, because you are required to get through it to advance the post-game. The reason why it's so challenging if you're a fire-type is because you have to go through it alone in order to find out how to get your partner back and the dungeon is crawling with high level rock and ground-types. Further complicating matters are two fire-types with Flash Fire (Growlithe and Houndoom), an ability that completely nullifies any fire attack you throw at it.
    • Going through Mystery Jungle as a Grass type is simply hellish; literally every Pokémon in there is a Poison type, with a fair few of them also being Bug or Flying type, and they are perfectly capable of ending you in one hit. Similar to the Sand Dune of Spirits, it is also plot-demanded and you cannot bring allies on your first visit.
    • In general, many dungeons and Connection Orb missions can seem like this due to the heavier emphasis on the Roguelike side of the gameplay. This seems to have been done to encourage players to swap their team members out rather than sticking with their player and partner. Since leveling your Pokémon is so slow, it's easier to do the harder missions with a team of the higher-level Pokémon that you gain access to early on in the game.
  • Ensemble Dark Horse: Shares a page with the rest of the franchise.
  • Fanfic Fuel: Now that we know that the events of the previous games all happen in a single timeline and relatively quick succession, there are two possibilities born from this:
  • Fanon: A very common theory is that Dark Matter is literally the same entity as the Bittercold from Gates due to their extremely similar origins and modus operandi.
  • Friendly Fandoms: Oddly enough, this game has one with the Undertale fandom of all things. Possibly because of some similar themes, and the Final Boss of both games involving forgiving them despite looking like hellfire incarnate on the surface, and that deep down, they're more sympathetic than they seem at first glance.
  • Game-Breaker:
    • The level 50 Salamence you can get five chapters into the story to use in side quests. Of course, you have to beat it at that low of a level first. And right after that, a level 55 Dragonite can be recruited, and this time without a fight.
      • Around that same time you can also do a fairly easy mission for Whiscash that nets you Alakazam, Tyranitar and Charizard. While Charizard isn't over level 50 like the others it can be re-taught Heat Wave to make it a powerful room clearer early in the game. And while it can be difficult a mission for Flygon can net you not only another powerful room clearer but also a level 64 Hydreigon with incredibly high stats and a solid movepool.
    • Any allies you have that possess Entire Room attacks such as Discharge, Ominous Wind, or Silver Wind. Rotom in particular has access to three of these types of moves in its natural moveset, can be recruited early, and once its alternate forms are recruited can be used even when the normal one becomes unavailable.
    • With the above in mind, lethal emera combinations such as Type Bulldozer, Barrage, any status-inducing emera.
    • The Ally Reviver emera. Keep your leader alive while using the others as meat shields. Not only do they avoid using Reviver Seeds, but the emera has an extra additional effect of fully restoring their HP, PP, and Belly amounts.
    • Blast Seeds. In the previous games, they only caused about 35-50 damage to an enemy (if eaten; they're weaker if thrown). In this game, they do a huge 100 damage. They can easily and quickly take out some of the harder enemies if you have enough.
    • Resilient Looplet and emera. It prevents the user's stats from being lowered by all moves, yes, including self inflicted moves (i.e. Draco Meteor, Shell Smash, Close Combat, etc.).
    • The optional dungeons that lower the party's level to 5 can be trivialized by bringing Djinn's Bottle. Because the bottle isn't affected by level restrictions, the player can let Hoopa OHKO everything.
    • Moving through walls allows the Pokemon to be immune to non-spread attacks and to be able to explore dungeons easily. Hence, Pokemon Mystery Dungeon penalizes the Pokemon by taking off five Belly points for each turn the Pokemon is in a wall. The Satiated Looplet removes most sources of Hunger, including the penalty for moving through walls—hence, certain Ghost-type Pokemon (or Darkrai) holding Satiated Looplets can bypass most dungeon challenges.
    • Toughness emera. One can easily sum it up as the entire reason emera are wiped clean after each dungeon trip. Toughness emera basically act like a Focus Sash from the main series, but the thing that keeps them from being Awesome, but Impractical is the fact that they stack on each other, and activate even if your Pokemon is already at one HP. Even with only three, you're very unlikely to ever die. If you get lucky enough to come across several of these in your dungeon trips, you won't need to worry about dying during it, as your entire party will easily become a group of Nigh-Invulnerable tanks!
    • Unlike the main series games, there is no 'Effort Value' mechanic in the Mystery Dungeon series. This means vitamins, Life Seeds, and Sitrus Berries will keep boosting a stat well up to the 255 hardcap (500 for HP) instead of only boosting it ten times. These items are surprisingly common drops from treasure boxes dropped from enemies in late game dungeons. Additionally, the vitamins can be bought for a single Gold Bar in towns, and you will acquire a lot of Gold Bars over time as you open chests and as your expedition rank goes up. With enough stat pumping, you can easily turn your starters (or anyone really) into a mini-Arceus that can easily one shot everything the postgame throws at you as they futilely attempt to love tap you.
    • Cofagrigus will trade five Reviver Seeds for one Gold Bar, when in Gates To Infinity it was two Bars for one Seed. You're not likely to run out of Reviver Seeds soon.
    • The "Type Bulldozer" Emera, which converts all not-very-effective or no-effect damage into neutral damage, as well as bypassing Abilities. Wanna be able to blitz through a Water-type dungeon with a Fire-type? Find this Emera and you're rolling easy. Just walked into a Monster House, and the only room-clearing move you have is Heat Wave/Discharge/Surf but some or all of the enemies have Flash Fire/Volt Absorb/Water Absorb? Not a problem! ...Just don't hand it to an Earthquake user if your other team-members are Flying-types...
    • The Water Looplet. This equipment allows you to throw an item and have its effects hit multiple targets as it passes thru them. The obvious benefit of being able to disable multiple enemies with Sleep or Allure Seeds. This looplet also prevents enemies from catching the thrown items, making the various spike items a very useful and reliable source of typeless ranged damage. What's more, you can effectively double the value of beneficial items as well, including stat boosters, by having a 3rd character throw them at two other party members. As mentioned above, abusing the vitamins to stat grind will turn a Pokémon into a unstoppable juggernaught, and doubling this tricks means doubling the potential game breakage. And with proper planning, you can get this tresure as early as Chapter 12, just in time for the Entei arc.
  • Goddamned Bats: Delibird. They're normally pushovers, and their Signature Move Present is a silly joke move that inflicts random, but usually moderate, amounts of damage, alongside a chance to heal the target instead of dealing damage. When Present is used by enemy Delibird, however, they'll immediately teleport from wherever they are to an injured dungeon Pokemon (i.e. one you happen to fighting right that moment) and give them a Present, which is guaranteed to heal them. They're still relatively non-threatening as enemies, but you can have as many as three Delibird drop out of nowhere - one after another - just to heal a Pokemon that you're fighting. This can be especially headache-inducing when you're fighting a Pokemon with the Pressure ability.
  • He Panned It, Now He Sucks!: GameXplain's "meh" review by Ted from BrainScratch Commentaries garnered a lot of criticism, mostly because he admitted to never really liking the sub-series in the first place and criticizing its core elements. It doesn't help that he admitted to never even playing any games in the series before apart from a brief part of the first.
  • Hilarious in Hindsight: Check the main page.
  • I Knew It!: Many fans predicted that Yveltal would be one of the main antagonists of the game, but were wrong about the petrification of Pokémon being caused directly by him, as believed due to his actions in the seventeenth movie.
  • It's Hard, So It Sucks!: The game's heavier, heavier focus on the Mystery Dungeon part of the crossover - with contributing factors like the slow speed of gaining levels, the lack of permanent IQ skills, and the very RNG-dependent difficulty that more traditional roguelikes are known for - has prompted this response from many people.
  • It's the Same, Now It Sucks!: The game has gotten flack for rehashing Gates To Infinity's antagonist and for reusing some assets, such as the music.
  • Memetic Mutation:
    • Players compare the partner's adoptive dad Carracosta to Shia Labeouf.
      Carracosta: Don't let your dreams just be dreams.
    • The out of context speech bubble a certain Cleffa says:
      Cleffa: I like shooting...
    • In the personality test, if the game deems you as a "likable" character, it will recommend you choose Mudkip, possibly in reference to "I herd u liek mudkipz."
    • Riolu plus Fennekin pairs, thanks to easily being the most common player plus partner team going off the fandom alone. If half the fandom isn't mocking the overuse of the pair, the other half is playing it straight and/or Lampshade Hanging the overuse of the pairing.
  • Narm:
    • Nuzleaf's weird (implied) Texas accent can make him kinda hard to take seriously, particularly after The Reveal.
    • It's very clear certain Pokemon models were given higher priority when it came to expressions over other Pokemon models. As explained on the main page, major Pokemon like Pikachu and Riolu have model reactions that generally fit the mood of the scene. Other, less popular Pokemon, however, have reactions that make you wonder if the development team was even trying. A special note goes to Chikorita's "shock" and "surprise" reaction though...
    • Dark Matter's rather emphatic reaction whenever it has a power-surge:
    OOoooOOoOOoHhhhHHh!!!
    • The use of Taken for Granite as a child-friendly replacement for death has been around since Pokémon: The First Movie, and this is not the only Yveltal to use it, but it becomes particularly strained here. Once the plot adds "the place you go to after you are turned to stone", the ability to fight your way out of being turned to stone, and a mysterious place where if you are turned to stone, you are turned to stone forever, it makes one really wonder if there could be someone that would not realize that this is death in all but name...
    • During the final battle, there's a cutscene where several of the flying Pokemon attacking the Tree of Life are turned to stone. The thing is, it's only the Legendary Birds- the non-Legendaries are perfectly fine. In addition, while the flying Pokemon are supposedly meant to be attacking the Tree, it's not actually shown- they're just shown flying around the Tree like a weird entourage.
    • After the player and partner are turned to stone, there's a cutscene where the person behind it all declares their identity and intentions to the world at large. Once that's done, some text tells us that the culprits' attacks on Pokemon began, and many Pokemon around the world were turned to stone. Given that multiple Pokemon around the world have already been turned to stone at this point, you'd be forgiven for looking at that text and saying 'Well, duh, we knew that'.
    • During the Wham Episode at the top of Revelation Mountain, Krookodile appears and is confronted by Raikou and Suicune, who blame him for turning Entei to stone. Once he notices your party, however, Krookodile calmly walks past the Legendary Beasts and they do absolutely nothing to stop him, not attacking, not cutting him off, nothing. This leads to the chain of events that causes Nuzleaf to betray you, Yveltal to show up, and everyone present being turned to stone, including Raikou and Suicune. And then later, they have the gall to blame you for this mess when they're the ones who let it happen.
  • Nightmare Fuel: Dark Matter itself. The thing looks like something between a cross of the Persona 2 Nyarlathotep and the Shadow Selves from Persona 4, and it's in fact so strong that it can outright TURN EVERY LIVING POKÉMON in the world to stone...including Mega Evolutions, normal Legendaries such as Entei, Latias and Moltres, Mythicals such as Deoxys, and even ARCEUS, THE VERY GOD OF THE POKEMON WORLD ITSELF. (!!) Nothing in any Pokémon game is anywhere close to this thing; it's almost like it's not even supposed to be here, let alone in any Pokémon game.
  • One True Pairing:
    • The player character and the partner, as usual, but possibly even more so in this game. It helps that, while previous games have Ship Tease moments, this game has some pretty heavy ones throughout the game, especially in the ending and after-game. At one point, the protagonist even refers to their partner as "That's my 'Insert partners name here'!". And then there's the sheer lengths they go to when trying to get their partner back in the after-game...
    • When it comes to the actual species of Pokémon that get shipped, expect to see a lot of Riolu X Fennekin pairs, thanks to the personality of the player and partner easily being able to transfer to either of them.
    • Among NPC characters, Buizel/Archen has its fair share of attention. It helps they are among the Expedition Society members with a higher amount of focus, and that they hang out together once you complete the post-game story.
  • Player Punch:
    • When your partner asks you if he/she can be annoying after the field trip into the School Forest, and you say yes (You can have perfectly valid reasons for saying so), their dialogue in response WILL make you feel like a complete jerk.
    • Instead of you leaving the Pokemon world to return to the human world, it's your partner who has to leave. It turns out they were just an aspect of Mew — the aspect that helped enable Dark Matter's return after the first time around. Now that they've allowed Dark Matter to find peace by accepting it, however, they've fulfilled their purpose and are no longer needed. As your partner Disappears into Light, your character is left crying on their hands and knees throughout the credits.
  • The Scrappy: Watchog. He has the partner (and soon, the player) pinned as 'problem children', which means that he constantly gives them grief for not being perfect even though they often have really good reasons for what they've done. He ignores Pancham and Shelmet's bullying, constantly inflates his own ego, and spends pretty much every scene he's in being unbearable.
  • Scrappy Mechanic:
    • The cooldown period that higher-level Pokemon sometimes go through after going on an expedition. This was implemented due to the fact that the player recruits many high-level Pokemon even in the early parts of the game, and seems to be aiming to keep the player from settling on a single team and never trying any other Pokemon out. However, since the cooldown seems to occur at random, and even happens to Pokemon that you haven't taken on an expedition recently, the mechanic is utterly reviled, to the point where some players stop playing the story mode and stick to playing on Pelipper Island once they've recruited the team they want.
    • Going in toe with the cooldown period mechanic, there's the fact there is no filter or sorting system to know which Pokémon are available right off the bat. You have to check one-by-one to see if a Pokémon is available or not, making adjusting team compositions every day much more annoying.
    • Dungeons like Calm Craggy Area, Reverse Mountain and Road To Primeval Forest can be really annoying because of all the extra Pokemon you have. They're not part of the party, so they don't have your tactics and they wander off and get lost quite easily. If they get knocked out, you have to find them and revive them instead of it being automatic. They can't pick up items, and you often have to backtrack because one additional member started fighting a wild Pokemon.
      • All of this also applies to Client/Guest Pokémon, which are required for certain quests. Unlike the aforementioned dungeons, these Pokémon need to be kept alive until their relevant quest is dealt with, while still having all the problems those additional Pokémon have.
  • Slow-Paced Beginning: It takes around ten hours to get anywhere with the plot. Until then, it's more akin to a Saturday morning cartoon.
  • Squick: Meta example. Look at the box art of the game. Does that Chespin realize holding on Greninja's tongue is directly giving the latter a taste of it? Doesn't help that Greninja looks pleased.
  • Suspiciously Similar Song: Mystery Jungle's theme sounds like something you'd hear in a Fire Emblem game, with the flute in particular sounding a bit like the series' main theme. Additionally, said flute segment somewhat resembles Courser from Homestuck.
  • That One Attack:
    • Yveltal's Oblivion Wing is a long-range, piercing attack that can wipe out half of your team in one shot and heal him at the same time.
    • Any attack with that can hit the entire room (like Ominous Wind or Silver Wind) when they're used against your party, especially if it catches you off-guard. You could experience a Total Party Kill before you even realize what's happening.
    • Hydro Pump is a very powerful move that damages all enemies in a 10-tile straight line. A single Hydro Pump from an enemy that's not even onscreen can easily wipe the entire party, especially if your team is lined up in a hallway. Fortunately, abilities such as Storm Drain and Water Absorb nullify this attack completely.
    • Pluck and Bug Bite are two moves that are very common among bird and bug Pokemon in later dungeons. They do mediocre damage, but allow that Pokemon to eat Oran Berries and Reviver Seeds right out of your inventory, thus damaging you, destroying your healing items, and keeping them alive long enough to do it more.
    • Debilitating or stunning status moves (like Hypnosis, Stun Spore, Supersonic, etc.) can be chained together against you, leading to extended periods of complete inaction. Good luck fighting against enemies that can paralyze, hypnotize, puppet and confuse you all at the same time like you'll run into in Mystery Forest.
  • That One Boss:
    • The aforementioned level 50 Salamence, if you fight it as early as you're able to. It's intended to be more in line of a Puzzle Boss, meant to be knocked out with Blast Seeds, but not only the game does not hint this at any point, especially being incredibly early into the game, Salamence's sheer power and high HP makes things difficult even if know what to do (requiring around 4 Blast Seeds if you throw them, or 2 if you eat them, putting yourself in danger of being mauled by Salamence's attacks). Be prepared to waste a lot of Reviver Seeds.
    • The battle with Yveltal, Nuzleaf, and the two Beheeyem is probably the hardest boss in the main story. The bulk of the difficulty comes from Yveltal himself, who uses the aforementioned That One Attack to hit from across the room, damaging several allies in the process, and heal himself. Woe betide anyone with a Grass-type as a player or partner, as it may one-shot you. You admittedly come into the fight with a plethora of allies... all but one of whom are Psychic-types, and therefore weak to Dark-type attacks. Guess what type Yveltal's other damaging move is? He can also use Roost to heal his HP by a greater amount than Oblivion Wing and often spams it when his HP is getting low. The other enemies—Nuzleaf and the Beheeyem—love to spam status effects and gang up on your guest party members. Since the enemies either resist or are immune to Psychic-type attacks and you have Psychic-type allies, your numbers advantage quickly means very little.
  • That One Level:
    • The Submerged Cave contains several powerful Water types that can easily be Demonic Spiders (Barbaracle can use Shell Smash and Ancient Power to boost its stats to insane levels, Seadra loves to spam Hydro Pump, and Lumineon of all things can attack twice in rain with Swift Swim), with frequent Rain to make them even stronger. And it's even worse if you or your partner are Fire types...
    • Mystery Jungle, a solo dungeon that comes in the post-game, is even worse, especially for a Water- and Grass-type player. It's filled with Venomoth (who can power themselves up with Quiver Dance and then wipe you from a room away with Silver Wind), Ariados (who can use Bug Bite to eat your Reviver Seeds and Oran Berries) and Trubbish (who leave Toxic Spike traps laying around everywhere). Worst of all, however, are the Haunter and Gloom, who can hypnotize, paralyze, puppet, and flinch you. If you're unlucky, and run into a Haunter that just feels like spamming Hypnosis, or a Gloom that decides to keep you both Paralyzed and Poisoned at the same time, you can die literally without ever getting the chance to fight back.
  • That One Sidequest: Gallade's request to have a letter delivered to Roserade. Unlike other letter-delivering requests, there's no place listed on the letter—it's simply listed as 'Out Adventuring Somewhere in the World', meaning that you essentially have to comb every continent every day to see if she's showed up in a town or in one of the cafés randomly. If you're lucky, Roserade will be standing a couple of feet away from Gallade, if not you could be searching for in-game months for Roserade to show up.
  • They Changed It, Now It Sucks!:
    • Fans were very annoyed with the fact that the option of nicknaming new recruits got removed, as it prevents personalizing team members.
    • The game has a limited amount of missions, rather than using the randomly-generated mission system the previous games did. Fans who preferred the routine of taking jobs and doing them rather than dungeon-crawling for dungeon-crawling's sake weren't pleased.
  • They Wasted a Perfectly Good Character:
    • Krookodile is said to be the biggest crook in Lively Town, and the Expedition Society can't do anything about him because he's too strong. He could have made another good puppet for Dark Matter, but he's turned to stone before he really gets to do anything. Had he antagonized the player more, had a boss fight, or had more closure as to what he was intending at Revelation Mountain, him giving up crime and getting a real job in the epilogue would have had more impact.
    • Many fans wished the other school children; Deerling, Pancham, Shelmet and Goomy had as much of a big role in the game as Espurr.
    • For some people, the player themselves is this. Since the player has no special abilities unique to themselves (like the Dimensional Scream), and since their amnesia and backstory as Mew's human partner from the past isn't explored much, their impact and relevance to the plot can feel strangely minimal. While this seems to have been deliberate, in order to focus on the partner instead, it also resulted in the player feeling very flat and boring for some.
    • In post-game, Carracosta. Some players noticed the absence of Carracosta, and were bothered by it, due to him being the parent of the partner Pokemon. Though we see the player Pokemon going through emotional turmoils at the loss of their partner, we don't get to see Carracosta's reaction with the loss of his child, which could've added more interesting scenes between himself and the player Pokemon in regards to the partner. Though there's a segment where when you go back to Serene Village with Mew, and he reacts accordingly, it's still watered down compared to how much the developers could've really gone to show how a parent feels and tries to cope when losing their child.
    • Quite a few Pokémon from older Mystery Dungeon games show up, among them being Ninetales and Absol from the original games, who tell you that they know of other humans who turned into Pokémon like your character did...and then they return to being completely ordinary NPCs who spout standard Welcome to Corneria-style phrases.
  • They Wasted a Perfectly Good Plot:
    • The Dark Matter issue has so much potential to make good guys suddenly turn nasty due to negative emotions such as jealousy or hatred, but you only ever see a meager amount of the victims (Nuzleaf, the random Beheeyem, and Yveltal) doing this. What's more, it's never explained how these victims turned out like this at all.
    • At the very least, Nuzleaf and the Player should've been seen hanging out more, so his betrayal hurts much more.
    • For those that dislike Dark Matter, Nuzleaf and Yveltal's entire reveal can feel like this. Since Dark Matter is explained to become active and inactive in cycles and that it is hunting for the Tree of Life, the game could have easily substituted Yveltal for the Big Bad and Nuzleaf as The Dragon rather than introducing another non-Pokémon entity.
    • You can visit the other continents where the previous Mystery Dungeon games happened. Does this mean you can meet or even team-up with the other protagonists? Nope.
    • On a similar vein, despite the existence of multiple continents and the focus on world exploration, the vast majority of the main story happens in the Water Continent. You only visit the Grass and Air Continents, and the Sea of Wonders for one chapter each, whereas the Sand Continent is only a required visit during the epilogue, and the Mist Continent is completely optional.
  • The Un-Twist: Nuzleaf is evil. This isn't much of a surprise to anyone who's played earlier Mystery Dungeon games, who've likely learned to be immediately suspicious of Pokémon that act overly nice.
  • Vanilla Protagonist: The player character is mundane to the other characters to the game; he/she does not go through as much character development, and he/she originally being human is downplayed in significance compared to other entries in this game series.
  • The Woobie: Your Partner. Nobody's really close to them, they're regarded as an annoying, stupid troublemaker, and some of your attempts to encourage them actually end up discouraging them further. It's especially hard if you picked Pikachu as your Partner, seeing the beloved series mascot treated like crap for the first time.
  • Woolseyism: There are several changes to the translation that become incompatible between Japanese and English, as seen here:
    • Mawile Spotting the Thread notices the imposter's use of Japanese Pronouns rather than grammar. In ther german version, Bunnelby is a Third-Person Person instead.
    • Dark Matter's speech alternates between romaji, katakana, kanji, and hiragana. The English translators had to make words have random capitalization to emulate a similar effect.
  • Win Back the Crowd: The reinstatement of many features that were removed, such as the Player Personality Quiz, as well as the announcement that every known Pokémon as of the game's release will be available, have done a lot to raise people's hopes for this game after the lackluster reception of Gates to Infinity. Whether it succeeded at winning back the crowd... depends.

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