I'm not a fan of the current good/evil dynamic also. I don't mind races starting good/evil though, and events/actions changing them, even if that means ditching some of the neat graphical effects that have been planned. Perhaps, kinda like FFH2, what happens to the world, whether it gets renewed or further torn, would depend on actions more then just your race?
That said, there should be a "victory condition" where you destroy the world through actions, and everyone loses. I'd like to see that as an idea.
Humans and fallen should be differentiated on their philosophy (Humans more collectivist, Fallen more individualist) and backstory, more then alignment. Then again, I've never though Stardock handles good/evil that way- it was ham-handed and poorly done in GC2. I got a feeling that player feedback may end up conflicting heavily with Brad's backstory ideas- in which case- which one will take precedence?
One idea with alignment: perhaps alignment should have indirect consequences as well, like how your citizenry behaves and develops?