Overall I like Wilder's Wonka better than Depp's, but I think there's a major misstep with both of them.
Wilder's Wonka, in the final scene, is a total jerk to Charlie, lying to him and being really cruel to him as a final test. That's simply not cool, and it's not the behavior of someone who likes children, as Wonka should. (Granted that Wonka only likes good children; he nonetheless likes 'em).
Depp's Wonka has that whole subplot with his dentist dad. It's not awful, and I don't think it's as bad as Wilder's sadistic Wonka; but it's much longer, and it couldn've been taken out algother without noticeably hurting the movie.
My wife pointed out that the book really doesn't have an ending: it's just "Hey, we're in the elevator, you win the factory, yay, the end!" and is pretty abrupt. Presumably both changes were made in order to fix this lack of an ending, giving a final act to the movie, a final challenge that Charlie must overcome.
I don't think either movie accomlishes this rather necessary task well; but whereas Depp's Dentist Dad is low-level distracting, Wilder's Wicked Wonka changes the character enough that it leaves a bad taste in my mouth.
Daniel