Alas, Poor Villain: Assuming Fou-lu in IV is considered a villain (as opposed to Complete Monster Yuna), he'd qualify in the "good ending". He recognizes he was blind to the importance of humanity, and Ryu realizes all Fou-lu wanted was to separate mortals from the gods, and always felt guilt for Mami's death. Of course, the manga subverts this in its Third Option Adaptation.
Game Breaker: using the Kaiser is a lot more tolerable this time, since you can EASILY stock up on Wisdom Seeds by shop in the Fairy Village. And find all the dragon summons? WIN.
Love to Hate: Yuna. Despite quite possibly being one of the most disgustingly evil villains in the franchise whose actions cannot possibly be defended, he's quite popular with the fanbase. Admittedly, the majority of that group wants to see him die in a fire for all he's done, but he's still widely regarded as one of the better antagonists.
Nausea Fuel: Fairy Drops. You start out thinking it's a stone or a precious metal. Turns out it's actually Solid Gold Poop, complete with a scene where the fairy is obviouslydropping a deuce behind a bush. Eww. Made even worse with Nina commenting on how "pretty" it is, and Scias being the sole member of the party even remotely disturbed that they're admiring fairy turds.
Nightmare Fuel: Take your pick: nuclear-weapon-like cannons that require human sacrifice; Nina's sister being turn into an immobile, immortal creature; or the fact that Cray was the one who had to mercy-kill her.
That One Level: Senesta, where the party must take on the exceedingly difficult task of chasing down an incredibly fast orphan.
There's actually a way of fighting them that forces them to use the attacks you want. Good luck figuring it out on your own though. The whole thing isn't helped by the annoyingly long dungeon (with puzzles) and even another boss that will have occurred between your last save point and I and II.