I think that attractions are better when they're created with their own characters. Think of the Tiki Birds, the Ghost Host, Chairman Clench, Figment and Dreamfinder, TimeKeeper, the Pirate Auctioneer, or the Yeti. All of them are very memorable characters who have their own attractions and their own stories.
The problem with film characters is that the narrative is generally complete at the end of the movie. The villian is vanquished, our hero gets the girl, and all is right with the world. Going back and trying to "recreate" the feel of the film with a "new" story thats just a re-hash of the original movie simply isn't as good an original story. Or, there's simply no way to make the plot of an attraction fit with the established canon of the characters (ie. Stitch's Great Escape, or Enchanted Tiki Room:Under New Management)
A good theme park attraction should be less of a narrative where you passively watch one event to the next, and better as an immersive scenario that you wander into and have the feeling that you're actually there in that environment. Using established film characters is much harder in the latter, because they take focus away from whats around you, and always have to be "doing" something to move the action.
The Pixar characters are great. But the worlds of Pixar are all fantastic takes on our own modern day culture. I think this is why they don't seem to fit into the "lands" as well. Buzz doesn't quite fit into Tommorowland as Woody doesn't quite fit into Frontierland. Despite being a space ranger and cowboy, respectively, the world they inhabit is the one of white picket fences and neatly manicured lawns of suburban America. The Pixar world is just a little too "clean". The environments of Pixar films are secondary to the characters. Even Monsteropolis isn't much different than a "real" city, despite all the fun details and monsterized versions of what we know. Compare this to the shrunken heads and jungles of Adventureland, or the dust and wood and cowboy hats of Frontierland. Those environments are living breathing "characters" in their own right, just as they are in the classic Disney films. Alladin couldn't take place anywhere else but Agrabah, whereas finding Nemo's Australian setting could be swapped for any industrialized nation.