I was considering making this a poll, but since I haven't beaten the game yet...
Anyway, mine is a toss-up between Yooka and Laylee themselves and Capital B. I like Yooka more than I like Banjo oddly enough. With Banjo, I get the sense that he's too slow to realize that some characters are jerks, whereas Yooka I feel is aware of it but tries to take the upper ground and be polite about it. Plus, I love Yooka's design.
Laylee is pretty much Kazooie, if only a touch more mean in some places, though maybe that's because some of the characters either don't notice or acknowledge her insults as opposed to Kazooie's. I also like that Laylee's smaller size givers her more of a spunk factor, since Kazooie was clearly the brawn in Banjo's arsenal and got most of the attacks and hard-hitting moves herself, while Laylee has the sonar thing, but she and Yooka work better as a team than individually.
And as for Capital B? I dunno, something about his very corporate personality and the idea that he goes about evil like it were a business (because it is to him) is very entertaining to me. Plus, once again, I just love his design! So many great, unique character designs in this game, I love it!
Who's everyone else's favorite?
...A Man can dream... Project Dream, that is.