I was thinking and the most logical would be to assimilate them into Empire as lower status citizens.
For me this has some kind of bitter aftertaste.
I think that there are other, more modern ways to handle this. Like a big ferderation with autonomous members which have different attributes. Like loyality, economic power, military power. The releation of a member to your empire/federation could be well-disposed, aspirant, loyal, core member etc. which imply different advantages to the federation and to the member itself.
Federation can't be easily implemented into a more or less traditional 4X, you need to conquer planets (and when you conquer a planet you suddenly end up with millions of aliens and you need to do something with them - genocide being uncool :)). Plus, I think federation could be done much better from scratch (not as 4X), check "The Last Federation" for example.
Anyway, even if, what about aliens living on another planet that has your race (multiracial planets)? Which is kind of a basic scenario, in real world aliens do not live on their planets alone, they always have some tourists, immigrants from other races and so on. Even if there is a federation system, it does not mean population would not mix (especially if we talk about them all being humanoids; come one, wouldn't you welcome some gorgeous Antarian girls in your homecity? :D).
The thing is, when you conquer a planet (and you do it a lot in 4X) you get planets with inhabitants. And... we need to think how to handle this scenario. It does not even need to be about political struggle, population happiness, etc (of course it could and probably should). But first I wonder how they exactly mix (can they use the same factories, what happens if there is food shortage is your original race starving equally to the conquered slave-immigrant aliens?)