From a long-time thread lurker:
The complicated part of integrating Pixar into the parks is that the majority of Disney theme parks—and certainly the Disneyland-style ones—recreate eras that don't exist anymore, or never existed in the first place. Pixar, on the other hand, is very contemporary, very modern, very now. The MK's lands are designed to evoke the wild west, storybook fantasy, or a sci-fi vision of the future. Every Pixar story takes place in the modern world, from Toy Story to Up.
The Monsters, Inc. and Buzz Lightyear attractions in Tomorrowland illustrate this well. Even if we ignore the obvious theming issues of placing Monsters, Inc. Laugh Floor in Tomorrowland, we can't overlook that the Monster's Inc. movie itself is modern, not futuristic. WDI set up the artificial construct of using the doors to pass into an alternate reality, but they would really have to offer time travel, too; technically, Mike would be dead in Tomorrowland. Buzz Lightyear gets a pass because the attraction exists in the imaginary BL universe, not the modern reality of Toy Story.
I'll extend this to the Finding Nemo overlays at Epcot versus Disneyland. The Seas pavilion doesn't pretend to be completely futuristic; and unlike its "Living Seas" predecessor, it doesn't even pretend to be a real seabase anymore. Guests aren't asked to believe they're in a storybook village or Jules Verne's Mysterious Island. Modern Nemo fits inside modern Epcot. At Disneyland, the Nemo Sub Ride is a great attraction in itself, but the theme is obviously shoehorned into Tomorrowland. Judging from online reactions to the ride's opening, most guests simply liked Nemo; DL fanboys foamed over the sub's return and lamented the Pixar inclusion; and many people enjoyed the ride, but felt something "just [wasn't] right." I suspect the last group of people were unconsciously reacting to the odd mix of modern Pixar mixed with futurism. The Nemo attraction simply doesn't belong there, because Nemo's environment is too familiar for us to accept as "Tomorrow."
The other issue is the Pixar aesthetic. I noticed the majority of signage for Toy Story Midway Mania uses hand-drawn, cell-shaded images rather than proper CGI-based ones. The reason is obvious: TSMM was first created for DCA, and the Pixar look doesn't belong on a 1920s boardwalk. To be fair, Pixar always offers some great 1950s-style illustrations to complement their CG designs, and WDI seems to use these properly. Yet the CGI aesthetic certainly wouldn't work in, say, Fantasyland, regardless of whether or not the movie were Pixar. Would WDI use CG images of Rapunzel, or would they ask the animation studio to develop a classic, hand-drawn look to harmonize with Fantasyland's old-world charm?
There's no doubting Pixar is here to stay, even though a few of their movies—*cough* Cars *cough*—are weak links in the Pixar chain. The company's strong storytelling and characters offered blessed relief to the designed-by-committee dross Disney Animation proper churned out from Pocahontas to Bolt. The big question is whether the postmodern Pixar characters and stories can easily blend into the classic Disney park culture. I'd say no, but room can certainly be designed for it—and should be.