I think if a sequel was to be made, it should shift its focus mainly on SP and I'm not talking about just a cinematic campaign. Diplomacy a more management should be included to add an extra layer of depth. Switch to a pure Risk-style turn-based system. I never enjoyed the one we have now. Perhaps allow formations to have a bigger impact, but surely with a prequel about the Republic vs. the CIS, ground combat will be much better.
(My opinions, not facts, my opinions.)