More ideas...
Just shooting this out there... how about ethinically tied structures as an option this might make trade grabing a little harder ...?
Galaxy Setup
1. For military wins add button below surrender called sudden death ie take their capital they have x turns to take it back and super sudden death you lose on loss of your capital. Maybe lower the military win multiplyer a little for sudden and even less for a super sudden death. Basically if you want to kill everyone quicker just add these if you want as options.
Choose Oppenents
1. When you select randomly pick races, still be able to pick a few races that you still want in your game. SO if you love Terrans they can be picked and everyone else is random.
Civilization Manager
1. The in the Civilization manager in the colonies TAB. I would just add one more thing. Structures. Basically this show what you have already build but I am not talking about structures under construction. Now different buildings would be represented with very small symbols or small letters. So basically you know if you put farms down, recruitment centers, Biosphere modulator, etc... You put your mouse over the picture, it tells you in text what it is. Cause this would help out in later colonization phase or in grabing enemy planets so you know what ya build and can stay in the manager longer and only go to planets that need attention instead of once every while double checking all your planets.
Ships
1, Longer names... I know I should abbreviate but god COME ON PLEASE LONGER NAMES! 
Turns
1. I think turns should be 2 weeks to a month... cause yes population boom is unreally but they say that ie terrans there is still a USA, China, etc... and every turn people leave to join your empire. But This would make it a little more realistic.
Quarterly Report
1. In the quarterly report ie journey begins. Customize it for every race. Its the first thing you read at the beginning of the game.
2. Oh ya almost forgot Top most powerful civilizations... Now when I KNOW I am on top and the game is goin to end with me winning why the hell does it show me at #2 or at the bottom... 20 bucks its has to deal with military rating and I know it
... Now if you conqueror someone it really needs to add military points to you. Same for the AI too when they chop off heads. 