Annoying Video Game Helper: Tails feels the need to remind you to save your game constantly, usually telling you to save before or after pretty much every major plot development, to point of being a Running Gag. It's clearly done intentionally too, since there's multiple points where you can have Sonic make him shut up.
Anti-Climax Boss: The Final Boss fight, Super Sonic vs. Imperator Ix, comes down to a series of easy Action Commands not unlike the ones you've been using for the entire game. Even if you mess Super Sonic's attack up (Ix fully heals if he isn't beaten in one turn with a perfect attack), the battle just gets locked into a stalemate with a low chance of you losing.
Character Rerailment: Knuckles in this game has taken more elements from his stoic, independent portrayal from the Adventure games as opposed to the hotheaded Dumb Muscle he was portrayed as in the mid-2000s.
Condemned by History: The game received decent reviews when it was released, praising its story, characters, and vast amounts of gameplay options. Its Dialogue Tree was also highlighted in positive reviews, seen as a way to give Sonic more depth and increase replayability. Many called it a bright spot in the Audience-Alienating Era Sonic was suffering during the late 2000s, the flaws in gameplay and story getting reported in reviews being dismissed as things to be fixed with a sequel, which the game's ending clearly showed was on the cards. However, said sequel never materialized due to a combination of lukewarm sales, its developer Bioware getting bought out by Electronic Arts, and an attempted lawsuit by Ken Penders, where he accused some of the characters as being copied from his. With Chronicles now doomed to be a Stillborn Franchise, what were once seen as minor complaints in the gameplay and presentation became much bigger issues with players now deriding its gameplay as severelyunbalanced with combat that focuses too much on touch screen gimmicks, requiring perfect or near perfect completion at all times to even accomplish anything. While the game's soundtrack and graphics were once seen as passable, they're both now seen as laughably bad at best. The Dialogue Tree has since been seen as unfitting for Sonic, with most of the choices doing nothing to affect the overall narrative aside from a Romance Sidequest with Amy. The vast majority of choices are limited to giving Sonic the option to be more of a jerk, which would be a common criticism of the character starting in the 2010s. The fact its lack of follow-up turned the Sequel Hook into a gigantic Sudden Downer Endingovershadowed any of the story's merits for many. Combine all these factors and Chronicles is now seen as one of the worst spin-off games in the franchise.
Dancing Bear: A lot of the hype the game got in development and upon release was purely because it was BioWare, best known for the Mass Effect and Dragon Age franchises, making an RPG Sonic game.
The Kron can be a major pain to bring down, since they're particularly resilient to damage unless you have certain POW Moves that can pierce their defense or hit their elemental weakness. Considering how finicky the commands for POW Moves can be, their fights can take quite a while.
The N'rrgal. Their leech attack doesn't damage you that much (especially if your team is leveled up enough), but they can steal health from one of your party members if it connects. No matter how much they actually end up damaging you, they can fully heal themselves and stunt your luck, meaning that all the damage you did to them could potentially be undone in an instant if they succeed in attacking you. Even worse, it's their default basic attack.
Disappointing Last Level: After a standard opening and a difficult middle portion in Metropolis, the end-game in the Twilight Cage is underwhelming due to the game's rushed development cycle. Chapters 7 through 9 are short without much side content, with the game rushing to introduce all of the alien races as fast as it can. Chapter 10 is more climactic, but also marks a big Difficulty Spike and leads into a sudden ending that is unlikely to get followed up on.
Enjoy the Story, Skip the Game: General consensus is that the game has some of the best story elements of a Sonic title in years due to Bioware's characterization, but its gameplay, particularly the battle system and overworlds, leave a lot to be desired.
Ensemble Dark Horse: The Ferox Chao, a unique Chao that allows you to skip the POW moves and land a solid hit. Equip them with Cream, and you will never have to worry about lacking PP or health. The Ferox has a unique design, and ended up appearing as a cameo in the IDW books due to Bobby Schroeder from the Thanks, Ken Penders blog obtaining multiple of those in a playthrough and Evan Stanley being a fan of the blog.
Fanon: An unusual case. Despite the game entering Canon Discontinuity due to the legal troubles surrounding it, much of its Worldbuilding remains accepted in the fandom by default, since no official work yet exists to contradict it.
Cream is by far the best healer in the game, especially if you give her the Chao that allows all of her special techniques to work without fail. Level her up enough, and Cream's PP-restoring move recovers more for the entire party than it costs her to cast it, allowing you to spam everyone else's strongest techniques without fear of running out of PP.
Knuckles has a serious claim to be the best offensive party member in the game. He has strong combat stats all around, two attacks per turn, and access to the best POW moves in the game for both AOE damage (Triple Tornado with Sonic and Tails, Knuckles Express with Shadow) and single target damage (Revolver Slam with Sonic, Echidna Rush with Shade). Him being put on his own team with Shade for the final chapter also means that he can take Shadow and Cream and have everything he needs to wipe out everything in his path without sacrificing healing.
Shadow has an attack that has a 50% chance of completely KOing an enemy. Equip him with a unique Chao that can give you a chance for an instant KO, and use his bonus level up points on his luck stat, and you have a force to be reckoned with.
The "Immortal Big" set up, especially against bosses. There is a rare Chao that forces enemies to attack its user. Combine with Taunt and Feel No Pain, and bosses will be forced to attack something that it can rarely hit or deal notable damage to. Combine with Cream's PP-restoring abilities, and most bosses are reduced to a joke.
Omega's cannon can do 200+ damage per hit: the Final Boss has 800 HP in his normal mode.
Nearly every single enemy in the second half of the game can act as this due to either ridiculous defenses, regenerating health, poisoning you every chance they get, leeching off your health, or any combination of the previously mentioned.
The Raptor Hawks. Although there's only six of them at the most, they have 120HP, do ~50 damage per hit, and can use "Evading" whenever they want. It's a good thing when they use their Special move, Feather Barrage, because it's easy to counter.
It's Hard, So It Sucks!: One of the criticisms the game received is how much it seemingly hates the player. The characters can have a hard time just hitting the enemies due to the high evasion of even the most basic encounters, said enemies can also hit like a truck even early on, and some of the Action Commands can get really complicated fast. There's a reason Cream is considered the best character in the game, simply because her healing can be required for some battles.
Magnificent Bastard: Dr. Eggman is Crazy-Prepared and resilient in his usual scheming. By planting a robot that could nurse him back to health, Eggman survives his presumed death before the game and presents himself as reformed when tracked down by Team Sonic. Despite lingering mistrust, Eggman keeps everyone on board by emphasizing their common enemy in the Marauders. Having built Metropolis, Eggman uses his knowledge of the city to hunt down the Marauders, even after an avalanche and a plane crash force him to use back-up plans. He also gains Tails' friendship by collaborating on upgrades to the Tornado and a device to banish the Marauders to their home dimension. With the team ready to chase down the Marauders, Eggman stays behind to ensure a safe return, only to instead build the Eggman Empire while his archenemy is away.
The game's generally poor/weird soundtrack (which is the subject of many urban legends over how it ended up that was) became a meme over time, with the theme for Central City (a high-pitched and dinky remix of Diamond Dust Zone from Sonic 3D Blast) being the most notorious.
Mis-blamed: SEGA received plenty of criticism for the game's shortcomings, even though the game was made by BioWare, who ran into a lot of Troubled Production regarding it.
Obvious Beta: SEGA's contract with BioWare expired during development and they shifted their efforts to Dragon Age: Origins. As such, the game was released in a late beta stage, resulting in a bare-bones RPG with essentially no real sidequests. One of the most noticeable problems is the music and sound effects; most areas use placeholder MIDI-format music of very low quality, and pretty much all sound effects in battle are placeholder noises.
Rescued from the Scrappy Heap: Big in the main series is at best a Base-Breaking Character due to his stupidity. This game makes much better use of him by having other people react to his inane comments appropriately, turning him into a much funnier character.
Executing POW moves and defending against attacks requires completing Elite Beat Agents-style commands with the touch screen. Depending on the move, the prompts range from manageable to extremely tricky, and for some, messing up even a little bit causes the move to whiff and waste HP. Likewise, many enemies can easily wipe out a party member if the defense prompt is failed. They're especially bad for players without a good stylus or touch screen.
Certain enemies can randomly choose to go defensive or evasive for a turn, making it either impossible to hit them or making all attacks deal Scratch Damage.
The "chase fleeing enemies" minigame wastes a lot of time at the beginning of the battle, and there's no option to just let them flee other than deliberately failing, which still wastes a lot of time.
So Okay, It's Average: The game has a good story and creative gameplay mechanics, but is brought down by a lack of content, unbalanced mechanics, and an awful soundtrack. It's generally considered to be at least enjoyable, but nothing excellent.
Special Effects Failure: The 3D gameplay models for the characters look very cluttered and uncanny (especially compared to what Sonic Rush and its sequel had to offer), with their lack of detail and disproportionately-sized eyes, and the other visuals alongside them don't look too good, either. The 2D in-game artwork is relatively better, but the animated cutscenes especially tend to look Off-Model relatively frequently.
That One Boss: Better hope you grinded to the point of invincibility before the penultimate fight with Ix. If you're not leveled up enough, don't have a good enough character combination, or if the equally annoying battles with Scylla and Charyb drained your supplies, you're gonna get your ass kicked hard.
Chapter 5 is one of the longest chapters in the game and forces the party to split into two groups to handle it. The party with Sonic and Knuckles has to reach Angel Island to deal with the Marauders and fight Ix, while the party with Tails and Eggman needs to continually fight through Metropolis' robots to assist them. Enemies are very tough especially in Metropolis (though Eggman is A Taste of Power and can carry his team well enough), and you have to choose which teams get the stronger party members like Cream and Big, leaving both unoptimized. This chapter is also the only chance to get Omega, who can be hard to find if you don't know where to look because of how tricky it is to navigate Metropolis.
Chapter 10 has the same challenges as Chapter 5 because the party has to split up again, but its most infamous point is when it recreates a typical Sonic the Hedgehogunderwater level in an RPG. Charyb floods part of Nocturne while Sonic's team is going through it, which drains their PP until it's empty and then drains their HP. Air pockets restore PP, but not HP, so Sonic has to rush through the area and avoid underwater fights (which lock out POW moves and fleeing) to reach Charyb.
That One Sidequest: The Romance Sidequest with Amy is fairly difficult to get even if you're trying to be nice to her, as rather than a set of flags or choosing enough nice responses, you essentially have to ask her every possible Dialogue Tree question at every point while agreeing with her every time the party has a difference of opinion in the story. (And her advice isn't always the most logical) The actual Relationship Upgrade event doesn't occur until near the final battle, so you won't know if you've unlocked it for a long time. It's very likely a player won't know it exists unless they read about it online.
They Copied It, So It Sucks!: While Sonic Chronicles stays within the main series' story, much of its plot is heavily inspired by the Archie Comics continuity, especially with regards to the echidnas. While some fans love the fact that Chronicles is the closest thing to canonizing beloved characters from the comic, others find it uninspired or unfitting with the main series.
The aliens of the Twilight Cage are interesting even if they mostly take traits from standard sci-fi races, as their designs are unique for the series. Unfortunately, the game starts rushing through the plot during the Twilight Cage section, so they don't get much focus and two of them (the N'rrgal and Zoah) have to share a chapter.
The playable cast with the exception of Knuckles stops having meaningful story content once they arrive at the Twilight Cage around chapter 6. Team Dark in specific have nothing going on for them once they enter the Twilight Cage besides an optional side-quest with Rouge; and one interaction of Shadow running around if he is not in your team, which is ultimately pointless. Omega nor Cream have anything going on for them.
While the concept of Shade as a former member of the Nocturnus Clan has potential, Shade doesn't have an arc of her own once she joins the team. She is mostly around to provide information to the cast about the Twilight Cage, and to talk with Knuckles a bit during the last chapter on his feelings on their kind. The game doesn't expand upon her feelings of leaving the Twilight Zone in the last act, nor how she feels about leaving behind her kingdom. At best, we have internal regrets of betraying Ix during one boss fight, but nothing comes out of this.
Despite Chronicles following up on the story of Sonic Battle, Emerl (and his Eggman-allied form from Advance 3, Gemerl) does not appear. The story only compares the Gizoids with Emerl in a scene.
The game takes advantage of both Tails and Eggman being Gadgeteer Geniuses by having them strike up an Odd Friendship while having to work together during Chapters 4 and 5. This had a lot of potential (as did Eggman being a permanent party member, just like Bowser in a few Super Mario Bros. RPGs), but he leaves after the halfway point so that he can instigate the Sequel Hook.
(of which a variation plays when getting ambushed in battles) is actually pretty great, as are the battle themes.