It is a shame that the game quickly loses minor factions as they get assimilated it would be better if those would be present until late game.


To do that I would suggest those things:

 - remove the assimilation quests

 - assimilation available only trough conquest or having "Cultural Flexibility" tech and absorbing the planet using influence once your influence zone reaches it.

 - expand interraction with minor faction so that it has significance during the game


This means that "ownership" or rather the alliance of a minor faction may change multiple times during the game and only during late game you will be able to assimilate them for good.

Maybe even a minor faction could be alligned with multiple factions?