I've played neither and hadn't even heard of Supreme Commander until now. I'm not big on war games. The only ones I've really played a lot have been Dominions, Sins of a Solar Empire, and Crusader Kings. 

I have a fondness for Dominions just because it's the most absurdly difficult and complicated game I've ever seen (300+ page manual, with a learning curve that makes that of Dwarf Fortress look flatter than a pancake). Sins of a Solar Empire just looks cool, keeps you engaged and often feeling overwhelmed, and has a decent storyline. And I just like Crusader Kings because assassinating annoying leaders, conquering every province you see, and assimilating entire cultures is disturbingly fun to do in that game.