Alternate Character Interpretation: The banter between Neil and Jane is either just friendly, or he could be flirting with her. Notably when she tells him to get a girlfriend, he winks and says "I'm working on it" - and alludes to Jane always picking on him in a Tsundere way.
Audience-Alienating Premise: An adaptation of a popular RPG video game series, that doesn't actually adapt any of the games' stories or characters? Many people suggest that the backlash wouldn't have been as severe if 'Final Fantasy' wasn't in the title.
Broken Base: A lot of fans were annoyed that none of the games were adapted to the big screen, while others argue that each game is unconnected and it makes sense that the film would be too.
Captain Obvious Reveal: The movie treats the reveal that the Phantoms are actually alien ghosts as a big reveal, despite the fact that "phantom" is a synonym for "ghost." Curiously, the initial version of the film (included in special features on home releases) shows that this plot point was treated as common knowledge among the characters in early drafts of the script, too.
Cliché Storm: It's widely accepted that the story and premise at least are original. However, the characters, particularly Gray (tough marine who rebels against authority), General Hein (Hate Sink of an authority figure) and Neil (Plucky Comic Relief) are hugely clichéd.
Designated Villain: The film has the problem that Hein is, for the most part, completely right in terms of his reasoning based on the known facts, and we're supposed to disagree with him because he's kind of a jerk and dresses like a Nazi. There's no proof Sid's plan will achieve anything useful (even he later says he has no idea what completing the wave will do, and his grand proof is that a tiny test rig has failed to kill one Phantom), Sid has been doing the equivalent of smuggling a live nuclear bomb into the last barrier city without telling the guy who's in charge of protecting it, and the council approves the construction of the Zeus Cannon, using a huge amount of no-doubt precious resources, and then hesitates to use it because of an objection that is primarily based on, of all things, Sid's new-agey religious beliefs.
Ensemble Darkhorse: Neil due to providing most of the comic relief. Steve Buscemi improvised most of his lines too.
"Funny Aneurysm" Moment: Neil jokes about hoping to have kids, to which Jane responds "that's a spooky thought". Not so funny when Jane physically has to watch him die.
Hilarious in Hindsight: In light of Roger Ebert vs. video gamers, Ebert gave the film one of its best reviews, calling it revolutionary in terms of its visuals and giving it a 3.5-star review. In fact, Ebert has given more positive reviews to video game adaptations than any other major critic, with additional positive reviews for Hitman, the Tomb Raider films, and Mortal Kombat.
Plot Hole: So how has nobody noticed the lake of glowing blue shit that's apparently a few hundred feet below the surface of the Earth?
Seinfeld Is Unfunny: By today's standards, the animation (especially facial) is nothing to write home about, but considering the film came out 3 years before the first movie in performance capture (The Polar Express)... well, at the time it was pretty damn impressive. It certainly scared the hell out of the Screen Actors' Guild when it released, who sent a few representatives out to talk to media outlets about how they didn't support the burgeoning rise of "virtual actors."
Strawman Has a Point: Hein's this-would-normally-be-true "Oh, so... if I point a gun at the Earth and fire, I'm not just making a hole on the ground, I'm...killing the planet?"
Hein is depicted as paranoid for suspecting Aki and Sid might not be on the up and up for sneaking the Phantom-infected Aki into the Barrier City repeatedly, despite that they have no proof their containment system won't suddenly fail, no safeguards in place if it does, and haven't told the guy in charge of security that one of them is a walking bomb that could compromise the city's security at any moment. Seeing this as a possible trojan horse strategy by the Phantoms is actually fairly sensible given the extent to which they both needlessly lied to him and the council about it.
Sid also tells Aki to burn any notes related to her support of the Gaia hypothesis because they might be used to discredit them as scientists. The problem being, Sid's objections to Hein's plan being based on a hypothesis he has never attempted to falsify and has next to no evidence for, and Aki's arguments based on intuitive guesses rather than hard facts, are actually pretty good proof neither of them is much of a scientist.
They Changed It, Now It Sucks: A variation. Plenty of Final Fantasy fans were annoyed that it wasn't an adaptation of their favourite game and hated it for being a standalone story.
Visual Effects of Awesome: While not quite as good as the hype was promising, lots of effort was put into the effects for the film, and some parts are quite impressive.
Woobie, Destroyer of Worlds: The Phantoms are stuck in a dream-like state, lashing out at everything around them, unsure of what is reality. The larger beasts are just gigantic wildlife that have no idea what's going on as well.