One theory is that the Academy's Liberal documentarians disliked the anti-union politics of Waiting for Superman, as well as Guggenheim's use of reenactments. (That didn't hurt James Marsh's Man on Wire.) Another is that the branch has historically favored underdogs over perceived frontrunners. While the branch has often resisted movies about showbiz and music, Exit Through the Gift Shop explores the state of the art world today in surprising, inventive and serious ways.
But I also like another theory: this year several films on similar subjects were competing for the same slots:
Waiting for Superman and The Lottery were both about the school lotteries. Neither made the cut.
Inside Job and Client 9 both interviewed Eliot Spitzer about the financial collapse on Wall Street, but Inside Job was more about Wall Street, while Gibney focused on Spitzer, who is not well-liked.
Restrepo was one film about the Afghan War that knocked people out with its soldier's-eye view of the fighting, while The Tillman Story was another that took place more on the home front.
Both GasLand and Waste Land sailed right through.