There was, of course, the visual fancy and the actors were in fantastical make-up, but because it was in Underland (Wonderland -- great explanation for the different names of the world), it worked perfectly. What I loved mostly was Alice, and how this was her coming-of-age story. It wasn't about the fantasy world, the boy she loved (or didn't), but about this young girl taking the reigns of her destiny ... in both Underland and our world. Mia Wasikowska was fabulous, delicately frail, with a steely underpinning that worked well for the character. Helena Bonham-Carter, Depp, and Anne Hathaway all created wonderful characterizations, and the voice work -- especially by Alan Rickman as Absalom -- were fantastic.
The issues that some seem to have with mostly boiled down to the fact that Burton did apply a real-world sensibility to it (the coming-of-age aspect), but for me that is what made it fly so beautifully. The marriage of fantasy and reality brought out the best in Burton, and I loved it.