Actually, they used final Cut :P In the beginning anyway, Crunch may be right about AE. One doesn't exactly exclude the other. Hopefully that's what we'll be using too, depending on our future access to school computer labs.
Basically, we'll be making characters without pupils and mouths and then put pupils, eyelids and various mouth positions in separate layers. We'll be doing multi-layer backgrounds too to allow people to pass behind stuff. We'll also export standardized animations (walk cycles, finger pointings etc) with a uniform background color (blue, for the most part) to be keyed out later. To have an excuse not to put much work into background art, we'll place the whole thing onboard a neutral medic submarine during WW2. Of course, if we want to, we can go to any other location we want to. In other words, not exactly full animation. If anyone has any advice it's very welcome.
There are a handful of people on this board I wouldn't mind working with on this, but you're all too busy and on another continent