Well, I think it's debatable how "nice" Kuzco did become at the end of the movie. Let's just say, they wouldn't be contradicting anything if some of his old character reasserted itself - especially when interacting with people other than Pacha.
Really, I think continuing on from the movie would be the wise decision - that way characters like Pacha and his family could continue to appear (I feel John Goodman's talents was a strong reason for the films success) and you could still get humour from the inner confict of the "old" and "new" Kuzco. Perhaps he could get his own "shoulder angels"
Plus it leaves the series open for more storylines - Kuzco is the ruler of the country which could result in invading army, arranged marriage, diplomatic visit, etc. storylines while Pacha is still in his village which could result in other storylines; weather problems, thieves, fierce animals etc. Add to this stories based on Aztec mythology, aliens (they are supposed to have influenced Aztec architecture - according to some!), witches and magic and there should be no limits to the imagination (and very few animal transformations!)
If I was doing the series, and this is just off the top of my head, I'd de-kitten Yzma (but it wouldn't quite work, so like the hulk in reverse she'd transform back into a kitten if she got too angry) and have her as a regular character (but not in every episode). I'd also set up a running joke about a Princess from a neighboring Kingdom being in-love with Kuzco (but her father wants to invade Kuzco's Kingdom) so they could appear in a few episdodes.
I'd also love to do an episode involving time-travel, and Make it like Back to the Future 2, with the "future" characters interacting with themselves in the original movie. Other ideas would be alien abductions, a travelling con-man conning Kuzco out of his kingdom, somebody damming the river and witholding the water from Pacha's farm and village, somebody discovering electricity, a feud between Yzma and another evil witch, a giant wooden robot... The list is almost endless.