I, myself, have never gotten a crossover idea past the planning and notes stage before.  I always ran into critical concept failures before it could become something of actual value.  Though, I did get a good chunk of balance insight from the attempts.  Learning from failure is a tried and true method of improving, after all.

In this case, I think I could make it work... but it would have to be altered enough to render it more of an "inspired by" rather than a straight crossover.  The smaller scale would be best rather than the grand scale that comes naturally to Supreme Commander.  It's easier to explain an exception than it is to rewrite the rules.

If Supreme Commander were to be crossovered strictly at a grand scale... Star Gate would be a better candidate... or either Gundam or Robotech.