I was going to respond to one of the comments but I decided to make it a post instead.
The majority of the animation for this film is being done traditionally; that is using a pencil and reams of paper. I believe that is the only way that subtle and successful character animation can be done.
However there are a lot of scenes that can more easily be done in Flash to help speed up the otherwise overwhelming amount of footage. These scenes have been layed out on paper, then scanned in, cleaned up and animated in Flash. One trick that I'm using for the flash animated scenes is to animate them on 2's so as better match the traditionally animated scenes.