Not keen on the real time idea...hate real time games and always preferred turn based....if the game goes real time I'm out.
I would love to see a in depth tactical ground warfare element, not talking hex based map or anything, just the ability to issues high level orders etc....expand the ground warfare and I'd be happy...also be able to issues tactics to your ships during combat which you can train them in to get better at them (esp at fighter level)...you'd have to use your imagination to think up different types of tactics that would be used, maybe look into modern ship combat tactics...or base them on WW2 tactics but in space at greater range, sure there is alot of info out there with regards to this.
Howabout chemical warfare....you meet a new race and then after capturing some be able o research chemical warfare against that particular species...so you can bombard them and wipe them out yet keep all their stuff......or it could all go wrong and they mutate into more powerful beings!!