So, I think it's very likely that any sequel / prequel to Star Control is going to continue to make use of the top down, real time combat, much like its predecessors.
Additionally, I've already made the point that the ultimate mechanics are pretty much a fighting game. The combat's a game of positioning, timing, reaction, and balancing strengths and weaknesses, while making use of the environment. Simplistic at its base, but with some pretty significant depth.
One of the more recent innovations in fighters has been to allow multiple characters, and to do a couple things...
First, to allow characters to perform 'assist moves' to exert pressure or extend combos, by having the character briefly appear and execute a move, exposing them to danger but potentially reaping massive rewards
Second, the ability to tag out with the primary character, possibly by performing an attack, allowing the match to involve multiple characters while controlling a single one
Third, the ability for health to regenerate when a secondary character is offscreen (within limits).
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I think all of these ideas could be used in Star Control's new game, but I'm not sure exactly what the best way to make use of them would be. Any thoughts?