Fat Gangsters. Their shoulder armor is highly resistant to physical attacks, so the reliable tactic of Hero Action, Jump, Shoot becomes ineffective. Unless you use Metal Coated Rounds, the way to win is to stay on the ground and attack from either the front or the back.
Any enemy with poison attacks, especially in dungeons, where the permanent damage to your life bar can really add up. Thankfully, you can be prepared for this, either by linking terminals that reduce/prevent poison to the dungeon, or putting Germ-Resistant Vests/Germproof Suits on everyone. Just make sure you remember to take a Rest at an Energy Station or at the Base once you leave; otherwise, your life bar won't fully recover even outside of battle.
In the bonus dungeon, any enemy with ice bullets. If their effect hit everyone before you can cure them it's game over, and since they have a bunch machine to deal big damage with them, things can go bad really fast.
Aetersyl, in Chapter 14. Players who have been reading walkthroughs to get past bosses may find themselves needing them to get past the first room, with its numerous, hard-hitting enemies.
Going to Neverland also counts, particularly if you decide to backtrack before the final boss. If you're already having a hard time by this point, you're nowhere near ready for the Bonus Dungeon.
Fandom Rivalry: With Final Fantasy XIII, another JRPGs released around the same time. It's also worth noting that looking at how this game separates Direct and Scratch damage and the way Ravagers and Commandos work in FFXIII is very similar. And both feature action-oriented battle systems that have few options and simple commands, but are meant to be tactically complex. A fan of the game once said "It's like it does everything FFXIII did wrong correctly."
An easily craftable item (Combat Scope β) can be sold for more than it costs to make. Add into this that the materials to create it are readily available from the Traveling Merchant and you have the recipe for essentially infinite money. This opportunity was removed in PC port.
Breaking your pistols is actually one of the main game mechanics. It doesn't show on the models, but in the inventory screen you can see your pistol decked out with ridiculous stuff like a drum magazine for absurd amounts of ammo before having to reload (really good, since you unload one cartridge with every attack), scopes stacked on top of each other, and multiple handles for decreased recoil.
Harsher in Hindsight: Pater's hand-drawn comic book and heroic speech are seen in a far different light when the events play out and it really does "cost him his life."
The tower, Basel, has the same name as a city in Switzerland. This makes it very difficult at times to take things relating to it seriously.
The game's customization mechanics don't show in combat, but let you stick an absurd amount of grips, barrels and scopes or sights upon your weapons. A minmaxed attempt can result in a mere pistol having nine barrels, four grips, three sights, a scope and an extended magazine. Gun enthusiasts would cry at how hilariously nonsensical this is.
Nausea Fuel: Thinking about just what that steak Barbarella is eating is made of. Hint: It doesn't have four legs and you killed it yourself (it was a fat goblin wearing an oil drum before it got steakified). Although you do get dog meat later on as Shop Fodder, which is slightly less squicky...
Zephyr is "good in the dark". That's great for fighting, not so great when Leanne wants to slap you for peeping, and also not great for when Vashyron wants to make innuendos.
Vashyron's dance, which to many people think his entire character is a Chivalrous Pervert. Project × Zone even ticks it up a notch.
Polished Port: The PC version released on Steam runs at 60 FPS, has resolution support for up to 4K, and has an optional 4K texture pack.
That One Achievement: There is an achievement for reaching Star rank in every level at the Arena. This requires you to win 500 battles. Not fight, win. Not necessarily difficult, but very tedious.
That One Boss: Cardinal Lagerfeld. Made worse by the fact that it's preceded by about 10 minutes of cutscenes with no chance to save afterwards and that you'll need a lot of trial and error (or a guide) to know which equipment to take (you can't change equipment without reverting to the pre-cut scene save). Also, you only have one character. Lagerfeld can teleport to get you behind cover and has a quick double-tap attack that can completely drain the hero gauge if you're not sufficiently leveled.
Wangst: While Zephyr's flashbacks do make his withdrawn nature more understandable, his threatening of Juris with a gun — who the team had just made a huge effort to save — and screams of "why can't I die!?" are more than worthy of a few cringes.
