First, I love the game! SOSE has helped me quit smoking. Because the game is so good, I can't take the time to go buy smokes. I can't wait for the expansions. Things I would like to see:
New races with new abilities and ships
New planet types
The ability to terraform planets - to increase population potential
AI that fights instead of running away
Single Player Campaign for each race WITH cutseens
Planetary defenses such as anti capital ship weaponary
The ability to zoom in to planet level and see the people/aliens running about - probably not gonna happen but I like the idea
The ability to trade, steal, or learn technology from other races
Phase lane mines or possibly a device to cloak phase lanes so that enemies won't see them.
Some of the things I meantioned were stated above by others. Some of the things I mentioned are in the 7 Deadly Sins MOD by DANMAN. DANMAN you are the man!