The Emperor's New School/WMG

This takes place before the movie.
In the movie, Kuzco was the emperor, in this one, he's training for it. It clears up the Aesop Amnesia. And, with selfish Kuzco, it makes a fair amount of sense for him to forget all the peasants.
 * Doubtful, since a lot of jokes and homages in the series came from the movie. The llama has been done.
 * And he already knows Yzma is evil.
 * And he and Pacha are friends, kinda.

Both levers are wrong...at first.
Kronk rigged them that way for a laugh. While Yzma is too busy getting out of whatever trap he laid, he puts in a code on a secret keypad to make one lever right. She just never bothers to remember which lever was wrong last time. When Kronk first had the idea, sneaky Kuzco came across a piece of paper with his code.

The female llama herder in the early versions of the movie was retooled into Malina.
Kuzco has no other Love Interests.

The Spaniards have already been visiting the Americas, and about to colonize.
Explains why they also serve Spanish rice and Swedish meatballs. And why they refer to their own gods as myths. And why Malina tells Kuzco being Emperor doesn't make him better.
 * Remember, the whole franchise has never been historically correct. What makes you think they'll start doing that with the series? And the Spanish rice and Swedish meatballs are just in the Anachronism Stew.

This takes place WAY after the movie
They're decendants of the movie ones. See above. There are also backpacks, elections, and robots.
 * ALL of them with the exact same name? And they all look exactly alike? And they have the exact same personalities? And if it's the future and they have robots and such, why don't they have cars or live in skyscrapers? Why do they still live in such close proximity to a jungle? Why do the guys still wear skirts, dresses and, namely Kuzco, huge earrings? Even now most people who believe themselves to be of Inca descent wear Western clothes at some point, if not most of the time. Again, remember the Anachronism Stew. The whole thing shouldn't be taken too seriously.

Kuzco is putting on a mask for public appearances.
Basically, as far as the entire kingdom knows, he still IS a spoiled brat. He's not ignoring the events and Aesop of the film, but instead keeping up appearances so he doesn't get swarmed for being the nice emperor-to-be. Can you imagine how many demands he'd be given once he took the throne if he was a nice guy on campus? He's being Genre Savvy, or something similar. The only problem is that he hasn't included Pacha and company on his plan.
 * That...makes sense. Wow; you just made Kuzco seem a lot smarter. Though it still doesn't explain his wish to have never become emperor. You'd think someone Genre Savvy enough to come up with this plan would know that you should Be Careful What You Wish For.

If a new movie in The Emperors New Groove series is ever made, this series (and Kronk's New Groove) will be declared Canon Discontinuity.
Because John Lasseter and his team believe that Disney should do their stuff for the art rather than try to make a quick buck off of it.