Two features I'd like to see.
First, in Rebellion you could assign characters to ships and planets. It would be good to be able to assign a commander character (Thrawn for example) to a fleet and they would give a bonus.
Secondly, I'd like to see an exensive scenario builder (but please make it more like the Blizzard editors so it doesn't require a good understanding of astrophysics and take a year to learn).
The scenario editor should be able to create scenarios and new planets to the campaign mode. What would be best of all though, a campaign editor feature (I really want to recreate the Thrawn Trilogy!).
Anyway, thats it really.