I saw Alice in both 2D and 3D. I didn't think the 3D added anything to the experience for me. The only effect I thought the 3D enhanced was the Cheshire Cat, who was my favorite character in the film.
Overall, I liked the film and think Tim Burton captured the magic and mayhem of Lewis Caroll's Wonderland/Underland. I'd be interested in seeing him go back and do a version of the original story since I was intrigued by the brief flashbacks of Alice when she remembers her first visit as a child.
The only things I didn't like was the dance the Mad Hatter did at the end and the accompanying dance music. It seemed as if the scene was an afterthought and was just dropped in and it took me right out of the film. Also, I didn't enjoy the song by Avril Lavigne (spelling?) during the closing credits. It sounded to me as if she was sitting on a pointy stick while she recorded it.
I am looking forward to when it comes out on Blu Ray.