I think that the big beef about all of the Pixar attractions in the parks isn't necessarily because they're *Pixar* but because they're based on movie characters, and they're expanding into places where Disney-character-based rides weren't before.
Another point is that Disney seems to have (for the most part) abandoned any project that might develop its own backstory and original storyline that is unique to the parks. Everything new HAS to tie in to a pre-existing franchise.
Haunted Mansion, Pirates, Big Thunder, Space Mountain, RnRC, Tower of Terror, Everest, Kilamanjaro Safaris, Kali, Soarin, Test Track, Mission Space. These are all great, classic attractions, none of which are based on a Disney cartoon franchise.
With the exception of Everest and Soarin, look at all of the recent attractions from the past couple of years that are based on a Pixar or Disney cartoon franchise: Laugh Floor, Stitch, Seas with Nemo & Friends, Toy Story Midway Mania, Gran Fiesta Tour, Cars Land on its way to DCA, the rumored additions to Pixar Place in DHS...
One final point is that some of these attractions (Stitch and Laugh Floor, for example) replaced *original concept* Disney attractions... Timekeeper and Alien Encounter were great, original attractions.
-Rob