I think MED can use Milkshape plugins, but better ask someone who knows how to model. I suck at it
Since Gamespace once sponsored a 3dgs contest I'm pretty sure it natively supports the 3dgs MDL format.

2D capabilities: I'm not sure if 3dgs is the right engine for 2d stuff, I'mnot really into 2d anymore. It's not impossible (there was a 2d game handed in for the witner contest) but there might be other software which is better suited for 2d (e.g. Multimedia Fusion).