Given the success of my last idea I think I'll dare to bring up another!
Currently in Galactic Civilizations it appears that you, when you invade a planet and conquer it successfully, simply eradicate the population down to last man and your soldiers become the appropriate colonists. Although it doesn't technically state that you've wiped them all out the way your remaining number of soldiers suddenly vanish and are replaced by surviving colonists of the exact same number heavily implies it.
This is certainly one way to do things but is, currently, the only way. I think this is bad when it opens up such a wonderfully large realm of possibilities while adding very little 'work' to the game as far as the player is concerned.
I think it would be interesting if, once a planet has been successfully pacified (that is, the number of your soldiers considerably outnumbers the native survivors), you could choose to allow them to live. This is something I could see the Terrans doing rather often, the Altarians, the Torians, the list goes on.
Moreover, Galactic Civilizations already has a precedent for this distinction: The very root of the Drengin versus Korath conflict. That is, slavery versus extermination.
Give us that choice.
Doing so would allow endless new possibilities. To list a few: Putting other racial bonuses to use (Terrans fielding Drengin Shock Troopers? Yes please!), the idea of assimilating aliens into your culture (perhaps the speed is governed by your cultural influence and other factors), possible rebellions should unassimilated native populations grow too large, an additional means of building and reinforcing Ideology (extermination, slavery, freedom), opening up the ability to liberate conquered populations of allies (for a MAJOR relationship boost since you could have just taken the planet), and the list goes on. That was just off the top of my head.
One more that I think I should mention is also quite possibly the biggest: The satisfaction of the players being able to do as they please with their defeated foes. Whether they want the sweet taste of vaporizing Drengin families for daring to start or war or maybe find great pleasure in bringing the Altarians under heel, they get to choose. No ambiguity.
I feel as though this approach works very well on two of the biggest fronts: It complements existing game mechanics by making a relatively small one and strongly complements existing canon, bringing more of the world of Galactic Civilizations from words to life in the actual game.
I'd certainly have no shortage of fun with this.