Something that bothered me in GCII was that there was nothing to differentiate a colony based on how it was obtained. If you colonized it, culture flip it, bought it, invaded it or it was given as a result of a peace treaty, they would all behave the same.

A solution I thought of is to use the approval system.

• colonies obtained by invasion would have a penalty to approval, that is if we don't commit genocide on the native population. Maybe this could be tied to the invasion events;
• traded for it would also have a negative effect on approval, I should note that in both these cases the drop in approval would go away if it stayed a number of turns under your control;
• culture flip worlds would have no penalty or a very small one, because they willingly joined you.

Something else that would be interesting is if a colony's approval would be very low, like say 20% or lower, it would leave your empire and either join with another faction or become minor civilization.