All Animation Is Disney: Like with the other hand drawn Dreamworks films, this film is sometimes mistaken for a Disney movie. In fact, one of the first things that pop up for the movie on a google search is questions of whether the movie was made by Disney or not.
Audience-Alienating Premise: A DreamWorks animated film about Euro-American contact only a few years after Disney's Pocahontas was bound to be seen as opportunistic and derivative by potential viewers. The premise could have attracted some following in Spanish-speaking countries, but the even larger number of liberties with the source material compared to Pocahontas instead alienated viewers there. An assistant animator on the film, Kevin Koch, claims this was a reason the film failed financially, believing from the start that a period piece film set in South America would be box office poison.
Awesome Art: You will weep for the death of DreamWorks' traditional animation department by this film's end.
Cult Classic: Received mediocre reviews and pulled some poor numbers at the box office during it's initial release, and several crew members have recently revealed that making the film was no picnic either. However, those who saw it in theaters as children have fond memories of it for it's quotable dialogue, as well as the fact that it was one of the only traditionally-animated American films from The Millennium Age of Animation.
Die for Our Ship: There used to be a site just for Chel haters, and many people on fanart and fanfic sites do give this reason for hating her. That, and that she's a "slut". That the one relationship she has in the film is with Tulio exclusively and pretty enthusiastically mutual, that her mode of dress is hardly out-of-place in her home, and that Miguel flirts lightly with most of the women he stands near never cross their minds.
Disney's Tangled came out 10 years later. Flynn and Maximus look like Tulio and Altivo.
Others have also jokingly compared to Thor and Loki. Which means they are gods. Especially funny since Miguel directed the first movie.
Ho Yay: And how! The relationship between Tulio and Miguel is extremely close, on the level of Like an Old Married Couple. From their naked bathing together and Miguel's jealousy at Tulio and Chel to their ability to communicate ideas without speech and Miguel's use of "the face" on Tulio, along with how very comfortable they are in each other's company. Indeed, some argue that the film works best if you go through it under the assumption that the two are repressed (or even not so repressed) homosexuals. It also spawned a (false) rumor that they were originally written as a gay couple and Chel was added in later (which was debunked when early model sheets and test footage popped up on the internet).
Moral Event Horizon: Initially, most of Tzekel-kan's unpleasant traits can be explained away by the in-universe culture clash - after all, what right have these strange, suspicious men to tell him how to run the city he's lived in all his life? Toward the end, however, he sells out his own people to almost certain butchery at the hands of the conquistadores, simply out of spite for losing his job, and it becomes apparent that by any culture's standards, Tzekel-kan is slime.
For those that like the Miguel/Tulio paring but don't hate Chel. It helps that Tulio and Miguel both go slack-jawed when around her, and that Chel flirts with both about equally, and of course there is Miguel and Tulio's extremely close relationship.
The movie has shown up on a couple of online lists of "Movies That Should Have Ended In A Ménage à Trois."
Special Effects Failure: A lot of the CGI in this film is really showing its age now and heavily clashes with the splendid hand drawn animation.
Despite a lot of the CGI looking rather dated now, the film has splendid hand drawn animation. The jaguar statue fight is the films real show stopping sequence, particularly for the jaguars animation—except for a couple shots, almost all of it is very carefully done hand-drawn animation.
The water effects for when the boat crashes in the films climax were a then-amazing and creative merger of hand drawn animation and computer effects.note They hand-animated one little clop of water splashing, multiplied it numerous times and composited it all together to give an illusion that they had painstakingly drawn all of that water by hand.
WTH, Casting Agency?: Not the movie itself so much as Elton John's tie-in Concept Album soundtrack. Rather than the original version of "It's Tough To Be A God" (which is on the soundtrack for the instrumental score), it features a muzaq-style duet with, of all people, Randy Newman.