mess around in their original .rel file and figure out which offset is the 1 that makes the characters (or the stage) 2D, and change that so that it becomes 3D. Mr Game and Watch comes up in 3D in BB, but due to his .rel file, it makes him 2D.
It seems that its a pain in the ass you have to do to for every character to make them 3d, Do I use Brawlbox to do it?