All good points, and belive me, its still in process as to how to go about this. The scaling for each class is going to be relatively general (80x80 for light mechs/gnd vehs/inf MUnits, 100x100 for med mechs, 150x150 for heavy and 175x175 for assaults) but as much as I kind of like having even a "fake" scaling to the units, I'm not convinced that the Atlas isn't a bit TOO big for the game. But thats why I have a crack bunch (or is that a bunch on crack...) of guys running em thru to see how they work in game.
And yea, the Atlas was modeled more on the Atlas 1 original rather than later Atlas's. How upgrades are going to be handled in the game is still a process under discussion. But it is likely there will be some units that will change appearance based on upgrades (Atlas, Marauder etc). Again, another firm waffling "hmmm, we'll see" )