First, "John Carter" – Disney has been very good about keeping quiet just how much of a Pixar movie this costly failure really was. But it was a Pixar film in everything but name only. The movie was directed by Stanton, who is part of the Pixar "Brain Trust" and who was at the studio as much as he could be – the film was almost completely pre-visualized there and when the studio decided to bring reporters into the editing bay to see how the film was progressing, they weren't flown to Disney studios proper, they came to Pixar. (Recent video of a Pixar animator showing how he helped direct the animators at Double Negative, the effects house that handled the bulk of the character animation on the film, substantiates this.) "John Carter" isn't nearly the trainwreck people make it out to be but it is proof of a Pixar-ian single-mindedness (highlighted by the lengthy New Yorker profile of Stanton) that can often get them into trouble.
It's this, "no, we can fix it" attitude that seemed to doom "Brave," originally slated to be the first feature at the studio directed by a female filmmaker (Brenda Chapman, of "Prince of Egypt" fame). With eighteen months before the movie was scheduled to be released, Chapman was unceremoniously removed and Mark Andrews, a writer and second unit director on "John Carter," stepped in to replace her. And unlike "Ratatouille," which was unified by the single creative voice of Brad Bird, "Brave" feels like disparate elements desperately clinging together to form a movie. No one knows exactly what happened or why Chapman was removed (yet), but it's clear that Pixar was unhappy both with her work and its own ability to create product that was at least up to snuff with earlier Pixar works. (Keep in mind this was around the time they altogether cancelled another project, Gary Rydstrom's "Newt," because of similarities to Blue Sky Studios' "Rio." Um, okay. Wasn't DreamWorks' "Antz" and Pixar's "A Bug's Life" in production at the same time? Thought so.)
The reasons for the sharp decline in quality and oversight are many – firstly, when Disney brought Pixar into the corporate fold, they installed many Pixar principles to head arms of Disney. John Lasseter, an executive vice president and filmmaker at Pixar, became the Chief Creative Officer of both Pixar and Walt Disney Animation Studios, as well as the Principal Creative Advisor to Walt Disney Imagineering (the folks that handle the rides, attractions, and pavilions at Disney parks the world over), while Ed Catmull, President of Pixar, additionally became President of Walt Disney Animation Studios. They both, presumably, have many more yachts, but their attention was now spread that much thinner – in addition to keeping an eye on Pixar's slate they were effectively running the creative side of Disney, overseeing things like "Tangled" and the scouting of locations for Disney's South American park (Brazil was the ultimate decision).
Also, many of the creative principles have moved on to other things, there has been something of a vacuum in terms of creative leadership. Stanton walked away (or at least down the hall) to direct "John Carter" and part of the way that Disney and Pixar got him to hang around for the "Finding Nemo" sequel is by offering him another live action movie (from Disney); Chapman, in her reduced role at the studio, has been removed from the Brain Trust; and Brad Bird left to direct "Mission: Impossible – Ghost Protocol," a huge financial and critical success that has left him in no particular hurry to return to the Emeryville animation studio. Bird has got at least one more live action movie on his plate – "1952," co-written by "Lost" mastermind Damon Lindelof and Entertainment Weekly reporter Jeff Jensen (though, it is set up at Disney). When we talked to Bird in December, he said that he's at Pixar as much as he can be, but we're pretty sure the only thing that would lure him back full-time is the promise of his live action Earthquake drama "1906" (originally planned as a Disney/Warner Bros/Pixar co-production) finally coming through. Other Pixar mainstays like Michael Arndt, whose original six-months-out-of-the-year commitment to Pixar has turned into a year-round affair, are drifting too – Arndt has been tapped to be involved in the "Phineas and Ferb" movie for Disney proper and contributed to Joseph Kosinski's sci-fi actioner "Oblivion" (probably when it was still at Disney) and next year's "The Hunger Games: Catching Fire."