No, why would it be? I usually don't pick favorites of anything, really, if I like something I'm fine with liking it and not putting a rank on it. The only reason I'd say Mew's my favorite is because that's the pokemon I always used to want to get as a child.
I don't watch the anime or read the manga, so I don't know much about them as characters. But I know that the manga has a completely different sequence of events and interpretation of character relationships than the anime, so I guess something like that should only be expected.