These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: Like most animated films today, the Power of Friendship is presented in full force. Unlike most animated films today, it manages to work in the movie's favor.
Ass Pull: Yzma and Kronk getting to the lab before Pacha and Kuzco, especially after being hit with lightning and falling into a ravine. Like everything else this is lampshaded.
Ymza: ... How did we, Kronk?
Kronk: Well, ya got me. By all accounts it doesn't make sense.
Award Snub: Whenever there's an argument about voice actors getting Oscar love for their performances (say Robin Williams for Aladdin or Ellen De Generes for Finding Nemo), Warburton's name comes up a lot for his work as Kronk.
Yzma's Villain Song "Snuff Out The Light" was for Kingdom In The Sun but was recorded before the animation even began. They couldn't use it for the movie since its exposition is different from the final products plot. The song was put on the movies soundtrack though, saving it from being a lost track.
Ho Yay: Kuzco and Pacha. Come on, you saw it. They had Kuzco dress up as a woman and pretends to be newlyweds with Pacha, Pacha almost giving him CPR and claiming "it was not a kiss", the amount of awkwardness between the two (including after they hug!), and Kuzco's Tsundere dynamic with Pacha. What more proof do you need?
The PlayStation, Dreamcast and PC game was just as humorous and satirical as the movie is, hanging lampshades on video game clichés long before The Simpsons Game did. However, there are changes to the plot, such as game Kuzco knowing Yzma is trying to kill him right from the start, while in the movie he did not learn that until after the dinner scene. Should also note that Yzma's crocodiles are, shall we say, more competent guards than they were in the movie.
Seinfeld Is Unfunny: Aside from the whole "twisted, snarky fairytale with an all-star cast" concept being monopolized by the runaway success of "Shrek'', this was also the first Disney film is years that didn't follow the studio's increasingly obvious formula. Anyone who doesn't remember that time will probably have a hard time getting back the "David Spade as a llama" gimmick.
Sequelitis: The direct-to-DVD Kronk's New Groove was dire, save perhaps one or two individual moments. The follow-up TV series The Emperor's New School regained some lost ground but had a tendency to take jokes from the original movie and re-re-re-use them until they lay in tatters.
Vindicated by History: The film was eventually a modest money-maker, and has garnered a new lease on life in the post-Shrek world as an example of how to do a timeless animated comedy right - many of the gags aged far better than the heavily modern pop-culture based humor of Shrek and its knock-offs, and the character of Yzma is now viewed as one of the best Disney villains.