I realize this may be a politically incorrect idea, but shouldn't there be contingencies to deal with the alien inhabitants of a world you took over? I just occupied 2/3 of the Arcean Empire by force. Now, I treat them reasonably well... I certainly don't want to wipe them out, they are taxpayers. But shouldn't the game be keeping track of how many of my colonists are Arceans vs. Humans. I mean, assuming these guys have voting rights (do they?), why are they ever going to vote for me?
Here's the suggestions:
1) Keep track of colonists by ethnicity (in, say, "population units"), with an ethnicity percentage based on the percent of the owning player's race living there, with a substantial modifier if more than two races are present (the more the merrier);
2) Give a race an influence bonus when trying to make your planet revolt based on the percentage of THEIR people living on the opponent's planet and the differential between their popularity and yours ("Don't look at me, *I* voted for Kodos");
3) Have a "colony policy" for each colony (settable globally through the governer) that has both ethical, morale, and economic advantages, say:
a) Egaletarian - full voting rights, equal taxes, other races count as yours does, ethical boost, costs more to maintain, you cannot send in any colonists;

Guarded - no voting rights, full economic rights, some loss of morale based on ethnic percentage, costs less;
c) Apartheid - no voting or economic rights, some loss of planetary production proportional to ethnic percentage, alien population does not grow as fast as your race's on that planet, more ethical loss, alien morale is strongly affected;
d) Manifest destiny - you are a monster, you take a big ethical hit, alien population drops proportional to your population's growth, big moral hit ("damn indians!), major economic losses until the population is less than 1% alien
d)
You can change