Alternate Character Interpretation: There are those who believe that Marche is really the villain and that he is essentially killing off a world full of people and stripping his family and friends of their hearts' desires in a selfish wish to go home. While the sequel more or less confirms that things worked out pretty well for everyone, it is true that the game isn't great about arguing against this point of view.
Author's Saving Throw: The Radio Edition addresses Marche's motivations and the nature of Ivalice far more in order to avoid the issues players had with the game. And the sequel confirms that, whatever else he did, Marche's actions in the story don't amount to genocide.
Broken Base: The game itself heavily divided fans of the Tactics series, mostly due to the new gameplay direction and the story. For every fan that preferred the permadeath and slower pace of the original Tactics, another liked the faster pace and changes brought on by introducing all the new races and classes. Meanwhile, fans of the original's dark political drama complain that the new story direction is a step backwards in maturity, while others prefer the more-straightforward plot and argue that its critics are complaining about the surface elements of the game without seeing the true depth of some of the more psychological themes and genre deconstruction.
Fans are divided regarding the legitimacy of Marche's reasoning to destroy Ivalice.
Designated Hero: Just for the record, there are a lot of fans who consider Marche a Villain Protagonist because he decides on his own (and fairly quickly) to destroy Ivalice and restore the real world, without trying to convince his friends or looking for a way other than destruction, although the story paints Ivalice as a Lotus-Eater Machine and gives the Aesop that dealing with your problems is better than hiding from them.
Draco in Leather Pants: Mewt Randell and the Li-Grim. Neither is necessarily evil, but they qualify in a sense due to people seeing them as more sympathetic as they are, especially considering that Mewt is mainly selfish and willing to make the laws harsher against his subjects' wishes on a whim.
Goddamned Bats: Sprites/Titanias (particularly those with White Wind), enemy Gunners or Illusionists (who can hit you from far away), and anything equipped with Damage > MP. The latter ability results in damage reducing the target's MP instead of HP, and, worst of all, as long as the target has any MP, they will not lose HP.
On the Les Yay side, we have Ritz and Shara who have grown very close to each other by the time Ritz tearfully throws herself into Shara's arms.
Jerkass Woobie: Doned does some pretty fucked up things towards his own brother, including destroying a present Marche needed to see Mewt, but at the same time, the wish he gets in the fantasy Ivalice (a body with robust health that can easily move under his own power) is rather big compared to the others. Kinda understandable as to why he loathes the idea of going back.
Ritz to a lesser extent, mostly during the time frame when Marche is on the lam. Her reason for not going back is because she hates her albino hair because she's constantly bullied about it. It's possible that being bullied enough has driven her to the point where she mentally broke down, which would justify her desire to not lose her now naturally pink hair. However, being with Shara and the other Vierra gave her enough confidence about her white hair and ultimately reached the point where she stopped dyeing it after returning from Ivalice.
Narm: Ritz revealing why she's refusing to help Marche... because of her hair color. Bully-magnet or not, differing cultural standards or not, complex over it or not, that's one of the silliest possible reasons she could have put out for what the Gran Grimoire gave her. Hell, Shara seems to be as confused as the player!
Ritz does go into further detail on this when speaking with Shara in private: she hates her hair so much because her mother is always sad when she helps Ritz dye it, which is why Ritz hates her hair so much, the bullying situation notwithstanding. Shara points out that it's more than likely the other way around; Ritz's mother is sad because of Ritz's contempt for her hair.
Ron the Death Eater: Marche is commonly accused of many things, from selfish disregard for his friends to a desire to commit genocide, that ignore his honest attempts to get them to face their problems and his frequent moral conflict over his course of action, regardless of the rightness or wrongness of his actions.
Out of the Totema bosses, Ultima can be this if you don't bring anything that resists charm, which this early in the game can be hard to accomplish especially if you don't know what's coming. Enjoy having your team rip itself apart instead of actually destroying the crystals for turns on end. Oh and if you brought a healer with with the Life skill, prepare to watch them undo all of your work in seconds by reviving the crystals. Of course you can also just wait for Charm to be illegal, turning this into a Breather Boss.
Tier-Induced Scrappy: No one likes Engineers. Their mass-status effect skills are potentially game-changing... but they're also completely random, and potentially hit friendly targets. This can be compensated for by ensuring the team is immune to the conditions they could inflict, but really, it's a lot of effort for comparatively less value than just using other classes and having them equip skills and items that make them better at fighting.
Vindicated by History: As of 2016 with its Virtual Console release on the Wii U, there have been some people who have pointed out that while the plot concept is adolescent (it was mentioned by several magazines it was like The Neverending Story), it actually has a lot of mature themes in it that a lot of people didn't notice in 2003 such as the effects of divorce on children, the stages of grief with the death of a loved one, bullying and the desire to retreat into fantasy as a coping mechanism, etc.
Viewer Gender Confusion: More or less invoked with just about all of the human characters, especially the generics - for the most part they're all androgynous enough to be interpreted as either male or female without having to make a separate model set for each gender.
The Woobie: Doned. Despite that he acts like such a little shit, he actually had the most reasonable wish out of all the four (which was to be able to walk again). And in the ending, he goes back to being an Ill Boy in a wheelchair. Despite getting friends, come on...
Crosses over with Jerkass Woobie, and it's a similar deal with Mewt - on the one hand, he seriously lacks confidence and self-esteem and misses his mother; on the other, he prioritizes his own comfort and feelings over that of others. Both characters (and even Ritz, to a degree) have understandable desires, but go about them with disregard for anyone who disagrees.