That's not a very good comparison, in my opinion. First of all: Alice in Wonderland would mean specifically the movie(s), where the books are called Alice's Adventures in Wonderland and Through the Looking Glass. And you didn't say either the movie or the book in either case, which is very important. Plus, the Alice books are very well-known, classic pieces of literature by a high profile author, where the Twilight books are new, pop-culture writings. Two VERY different things.
I'm not sure I could make a choice between the two, because they're not really similar enough to compare. All I have to say is: the Alice books are better books than the Twilight books (although I really like both... But I've only read the Alice books once, and I've read Twilight several times). And as far as the movies go- I never liked the animated Alice, and I've only seen the new one once, so I can't really say. But I did honestly like the Twilight movies when I saw them...