Cross-over is one of those things that feels like it should be easy to get right, but is gotten wrong nearly every time I look.

I'll admit I don't know jack about supreme commander, but I'll assume you did all the obvious stuff. You took two worlds that were largely compatible and with similar tones. I've seen people try to do Finding Nemo/Saw crossovers and it just doesn't work because it's impossible to maintain the lightheartedness of FN with the kind of horror Saw offers.  

The main point of doing any kind of crossover is usually to get certain characters in front of each other, but it sounds like you more want a world VS world thing. Perhaps your story shouldn't be about armies, but squads of people. Not everyone in star wars has capitol ships. Luke didn't have access to all the cool stuff until he teamed up with the rebels. Maybe instead of it being the big military factions from both worlds, maybe it could be about two smaller squadrons that don't have access to the full spectrum of cool gear both worlds offer? Maybe an asteroid took out a rebel/imperial ship's power, and a squad from Supreme Commander got separated from the rest of their troops. Now the two of them are racing to find a power source so that they can return home.