If you can film in 3D with a stereo camera, do it! It's so much better than post-processed 3D. The 3D effect in Alice in Wonderland always felt a bit out of place. And I'm not talking about composition, but rather about the tiny depth differences in details you probably don't get exactly right when doing post processing. And Burton probably was more careful than others will be in what looks like studio-driven films.
Ok, acknowledged, the comparison is everything but fair. Avatar had a much higher budget, which shows. It created probably the single least intrusive 3D experience for me so far. For purely animated films 3D is an easier task, and there Bolt felt almost as good as Avatar, Up a bit worse, but still so much better than AiW.
Many films still fall in the old pit falls like trying to shock / "interest" the audience with cheap sticking-out-of-the-frame tricks (My Bloody Valentine as a very negative example). Which bores at best, but certainly draws you away from the film. If it's done just for fun at the beginning of the film like in Monsters vs. Aliens, all right, but please behave. In Avatar the 3D effect was never annoying, it just drew you into the film and let you forget that you're watching a 3D film. It just fit.
Ah, and before I forget it:
The single most important feature of movies filmed in 3D is not the 3D effect. It's the fact that due to 3D directors and camera men finally have to think of good camera paths and slow cutting pace again. No chance to create "dramatic" effects with wacky camera and half second cuts, you have to have actually good choreography in action scenes. Otherwise the audience will... I'll spare you the gory details
Note that I still believe that the film content is way more important than the style. Still, we're talking about moving pictures, they ought to be pretty...