Ass Pull: The ending where Lincoln's Memorial is one of Thade, and apes rule Earth in the present day.Helena Bonham Carter has said she pointed out to Tim Burton that the ending made no sense after reading the script, to which he grinned and said, "I know, isn't it great?" Although impressively, Carter herself was later able to come up with an explanation that actually makes sense.
The scene in which Leo returns to a present-day Earth where everybody is an ape otherwise dressing and acting in every way like humans is impossible to take seriously.
The hero trying to pull off "no man left behind" on a chimp. It would be one thing if he was presented as a Friend to All Living Things, but instead of that, the movie treats it with all the seriousness of Generic Movie Hero Behavior. The confusion about the fact that it's all about a random trained animal makes it hard to treat the scene seriously.
Older Than They Think: The infamous twist ending was inspired by the original novel by Pierre Boulle, where Ulysse escapes from Soror (the literal eponymous planet) and returns to Earth, only to find that it was also taken over by apes in his absence.
Rooting for the Empire: Sure, General Thade is a right bastard who tries to wipe out humanity, but it's easy to admire him for his martial prowess and Rank Scales with Asskicking status, devotion to his father's legacy, and ability to actually get shit done compared to the sleazy ape politicians. Plus, unlike the dull-eyed hero Leo he's at least displaying some enjoyable pathos.
So Okay, It's Average: The general consensus of the film's reception is mediocre. The effects, music and visuals are worthy of praise, but it's all hindered by bland heroes, some strange performances and the infamously confusing ending.
Squick: Leo the human kissing Ari the chimpanzee on the lips. Granted she's not exactly a mindless animal, but still...
Tear Jerker: Thade's moments with his dying father, Zaius. Rather than telling his son that he loves and is proud of him, Zaius wastes his last words cursing humanity.
Took the Bad Film Seriously: Tim Roth and Michael Clarke Duncan are clearly devoted to this film, particularly Roth who gives the role his everything and makes Thade a legitimately compelling, charismatic and complex villain who is both a loathsome fanatic and xenophobe and a sympathetic figure who honestly believes in what he's doing.
Vindicated by History: Downplayed, but with the theCaesartrilogy having brought balance in the franchise and the onslaught of franchise media that relies on easy nostalgia, some fans have looked back to this film more kindly, with an appreciation for its effort to do something genuinely different and in Burton's own style rather than simply copy and paste the original, even if some of the writing choices such as the ending are still very divisive.
Visual Effects of Awesome: The only aspect of the movie that exceeds the 1968 one, particularly regarding make-up.
The video game
Complete Monster (PC/PlayStation version): General Ursus is the leader of the gorillas and one of the members of the Ape High Council. Seeing gorillas as superior to other apes, Ursus discovered that Professor Cornelius managed to find a way to use human DNA to improve the ape genetic code. Forcing Professor Cornelius to work for him and continue his experiments on captured humans, Ursus planned to "enhance" the gorillas and create an unbeatable army, which he intended to use it to completely wipe out humanity and take over the ape society, while slaughtering any ape who would resist his rule. When Ulysses humiliated him and stole the results of Cornelius's research, Ursus ordered his gorillas to attack a human village and wipe out most of the humans there.
Demonic Spiders: practicality all the apes are this due to how hard they hit, their ability to block your attacks, and the fact that they are all over the game.
(full version here