What do people think about the possibility of having the civilizations being unique for each planet one takes over. So when the Drengin invade and enslave an Altarian or Human colony they'll actually have the Altarian/Human populations on those planets and can enslave them, assimilate them or kill them off...
Kind of what Master of Orion 2 had but with the option to enslave parts of a population and relocate them to planets to be enslaved on so our "superior" race can thrive on their own worlds. I know this could interfere with the planet invasion concepts but the population number could instead take the effect of having a percentage of the population be the defense for a planet than the entire population (which is killed off when you invade).
This could also make the effect of poison cloud attacks actually kill off the population (depending on your play style). So in general this could have the effect of a higher level of control for your empire instead of it being the one population number for everyone.
Just a concept (I still like the previous system but want to see what other people think of this as well)