I think Wilder was more likable in the original Wonka movie, that's all. I like Depp in a lot of stuff, but in Willy Wonka, I thought he was kind of creepy.
You are not alone in this and I think for me personally its that I know too much about him as a real person to consider him anything like a real Wonka. Something just does not chime right, now as for Alice I did watch it and it was mostly enjoyable but something was still off with that too, just not as much as Wonka was.