Favorites:
1. Piplup.
2. Oshawott.
3. Jigglypuff
4. Psyduck
See the pattern?
Least Favorites:
1. Cilan. They BUTCHERED his personality. (Pun intended, yes I can making cooking puns too!) In the games, he's a shy, timid, and modest about whether or not he's a good trainer. In the anime, he brags non-stop about "It's Evaaaaluation Time!~", to the extent that he made an enemy, Burgundy, who was offended by how he incessantly critiques her.
2. Drew, May's rival. Right before the end of the Advanced series, May witnesses Drew mistreating his pokemon. Yet this was never elaborated on, never explored any deeper than Drew having a dark side. I didn't feel like this issue was resolved well, either, especially considering how he was still able to triumph over May, our ambassador for the ethical treatment of Pokemon.
3. Giovanni. Unlike the games, he's merely "the boss" who Team Rocket gets orders from. He's never truly confronted.