I would have put it in your thread, but I didn't want to just talk about the concepts of invading planets (Like I said, that was the third time I did that, and left out quite a bit, like)
Two new techs, which would lead to the alien populations going away. A 'Good' tech, that would all through genetic alteration, Terrans and aliens to interbreed. With a explanation that it use to be taboo, but people have the right to choose who to have children with. Since there would be more Terrans then any alien race in your own colonies (I get into this a little later), the interbreeding leads to Terrans with alien charactistics, but are still Terrans.
The 'Bad' tech would cause a secret sterilization of aliens in the form of a virus. This would then lead to a 'cure' in exchange for working for lower money. It would increase productivity, and keep the alien population down. To simplify this, to be cured, the alien has to work (slavery anyone) for the government.
Planets that defect don't gain Terran population unless you move Terrans there threw colonyships or transports.
(My reasoning for zero Terran immergartaion to the new 'alien' colony, is that they came from a crummy empire to begin with, so there colony isn't that desirable).
And, for conquest, after you when, there should be three options for you. First off, the new alien population on the planet should be some randam number generated based on what kind of attack you did (conventional, core detonation, mass drivers, etc.) and the population of the planet when you attacked. Your options would be:
Good: Spend money to improve the lives of those who survived. Your at war with the government, not the people. They suffered enough.
Neutral: Leave them to themselves. Why should they be treated better then Terrans. They can manage.
Evil: Exterminate the race. We are trying to cleanse the galaxy of them, not have them suck on the teet of our welfare system.
I know this is a lot of stuff, and I don't even expect it to happen in any GalCiv patch (but I'm still crossing my fingures) but this would be something great for GalCiv 2 or another expansion (theres no rule that you can only make one. Mabye another free expansion, or a really cheap one you can only download).