So basically here is my take.
Emperor's New Groove- I have absolutely no complaints about that film. It's hilarious from start to finish and Yzma is one of the funniest Disney villains ever.
Atlantis: The Lost Empire- I love the dark, gritty sci-fi adventure feel that this film has. I think the characters are interesting and the depiction of Atlantis is absolutely stunning.
Treasure Planet: There is a lot I like about this movie. The music is beautiful, the animation is beautiful, the characters are very well written, and despite the strange setup, the film does a surprisingly good job of staying true to the source material. I can see why people don't like BEN, and I did find him a little annoying, but I didn't let that ruin the movie. I actually find Silver to be one of the most likable and sympathetic Disney villains and I like the father-son relationship he builds with Jim that ultimately leads to him redeeming himself. In fact he's one of the few Disney villains who actually gets redeemed.
Also, Captain Amelia is awesome!
Captain Amelia is awesome!