I mentioned a few things in the chatbox while on semi-vacation. Will make this short:

While Dolby Atmos is capable, Monsters University simply did not take enough advantage of it. There were just too few scenes, as the movie was storyboarded / directed, which required use of precise positional audio cues, particularly form the sides or the back. 99% of the action in the movie was in front of the viewer / camera, so all the fancy Dolby stuff would have been highly inappropriate if it had been used.

I suspect this is not too different from Brave, which supposedly was 90% 7.1 and 10% Atmos. It comes down to how hard they want to work on the Atmos audio stream.  Perhaps Man of Steel (with action all over the place around the viewer) would have been a better movie for Atmos.

That being said, the two or three scenes in the movie which made good use of Atmos were kind of neat, .e.g. the frisbee being thrown from the center of the screen over our heads on the left side, the monsters in the "coliseum" scene, etc.

In the end, the Atmos thing was a slight disappointment. However, the El Capitan theatre and the overall experience was not and well worth the $26 VIP ticket (included 3D, pop-corn, drink, performance from a really good organist, live Disney cheerleader squad, cute animated short, and just being able to see the art deco theatre)