Well, I had no trouble suppressing the rebellions... I had vastly more firepower than any rebels could hope to match, but it takes a good chunk of time to put them down, and it was more annoyance at the fact that they re-rise ad nauseum every time I put them down and were in open rebellion 6 out of every 8 weeks, despite getting crushed every time.
I conquered the homeworld, which caused the empire to cease to exist, and magically all the rebellions stopped and all their fleets became docile and joined my empire. The homeworld never rebelled once, despite having 20 billion population--as soon as the empire was destroyed, the homeworld and the rebellious colony both went into positive happiness.
It sounds like they gave up when they no longer had an empire to defect to. If you looked at the happiness factors I think it said that they were angry about the war with their own race, that they yearned to be ruled by their own race and that they were unhappy at being conquered. It adds up to a lot.
Overall I think it's fine that they show willingness to fight for their freedom, there is just one thing I think would improve realism/challenge significantly from this aspect of the game:
Add a degree of pacification from the presence of enough soldiers to obviously win, then perhaps have their dissatisfaction be expressed through sabotage invoking a tax penalty without chance of rebellions, then have them wait until the time the empire weakens (or troops leave at least) and then do a violent uprising.
The problem with the way things are now is that they fight so much that they cripple their own population and prevent eventual freedom. I've sometimes ended up killing billions simply because I INSISTED that they pay taxes, so they kept rising up and dying futilely.
A fun option would be having a big world like that join an opponents invasion with a full uprising added to the other empire's troops.
< Message edited by Tehlongone -- 7/14/2013 2:58:50 PM >