Two suggestions

[ChildServices]

For current Distant Worlds
1) In the policy screen when you set a colony's minimum number of troops, that should tell the automation AI to garrison that number of troops so that it doesn't have to repeatedly build more every time your fleets come and steal troops which should instead make up the planet's defence force. At the moment, this option in the policy screen is fairly moribund and you're better off just doing it yourself, which can result in some rectal irritation on the largest maps towards the late game.

Unless of course, the AI actually does this and I'm just not making use of the automation properly. In which case, ignore this one.

2) Add an option that will make divisions of soldiers be named both with their race's troop names and their planet of origin.
E.g; A regiment of Boskaran Executioners will be called "Boskar 9000000000th Boskaran Executioners" or "9000000000th Boskar Boskaran Executioners"
This doesn't affect the game much, but I've been playing a lot of Victoria 2 lately and well. . . Renaming all of my regiments manually for flavour reasons is a bit of a pain in the ass. >.>

EDIT: A third
3) Make aliens who're living under the "enslave" policy that are killed during rebellions count towards your victory conditions as aliens that you have exterminated.