I have to say, I had my disappointments with the film. I think a more abstract screenplay with the same cast and visuals would have benefitted the film enormously. But the biggest complaint I see from those who hated it (besides Burton and Depp work too much together) is that...it didn't look good in 3D.
So?
I must be the only person in America who saw Avatar in 3D and went "Well, that was nice...I guess." 3D just doesn't enhance films for me. I saw Avatar a second time in 2D and the movie was no better or worse for it (albeit, the quality of its story and the creaks really are more visible upon repeat viewing).
I guess what I'm saying is that whether a movie looks good in 3D or not should have absolutely no baring on the quality of the film. Other than James Cameron films, chances are whenever you see the words "3D" in a commercial, you should just assume studio gimmick. If the film is good, 3D will neither enhance it or worsen it for the lack thereof.
Alice in Wonderland is a mixed bag of a movie, but 3D is the least of its problems and its absence didn't take away from its successes either.