To make 3d in 2d, you can't just draw frozen pictures. You need to animate the perspective to show (as mentioned earlier) the Z axis.
It's easy, but the further you get with your movie/contraption/experiment, the more details you want to add, and then it easily get's complicated due to the million layers you need to change, everytime you change the camera a single bit.
But in my oppinion, 3d made in flash looks better than 3d made in a 3d program, since no one can actually figure out how to make anything look good in those programs.
You should take a look at the remade version of Pico, for some inspiration.