What marks Pixar out from all the other animation studios is that when the story isn't working they're willing to throw away millions of dollars to fix the problem. Ratatouille, Wall-E, Up, they all benefited from this. All the other studios seem to be afraid to face up to story problems and fix them, figuring that they'll probably make back the money in any case (and they're probably right), but that's why Pixar make art, and the others make kids' movies.
And yes, I include How to Train Your Dragon - I don't get what people saw in that film, which seemed to be yet another by-the-numbers Hollywood father-son bonding flick. (cf Cloudy With a Chance of Meatballs, Madagascar II, etc etc). Plenty of good moments, very watchable, but nowhere near on a par with Toy Story III, let alone Up or Wall-E.