Edit: Originally this was meant to be a response in another thread on late game predictability. Reads a bit strangely without that context, but what the heck....
As much as I hate to flog other games here
...
Some of the concepts in Europa Universalis seem to work quite well. Each province (city) has a percentage likelihood of revolt which increases with war, religious differences, instability of government and so on. If they revolt and you don't suppress quickly enough they form a new country or join someone else. The larger the empire the harder it is to restabilize it after wars, etc. IIRC this can end in civil wars or a number of breakaway countries.
You also build up hatred from other countries depending on how you treat them - reducing your chances of diplomacy.
And you get badboy points for going to war and taking over other territories. If you get too many too quickly, you do get the rest of the world ganging up on you - but if you do everything diplomatically - you can avoid that. I like the way this requires you to maintain some balance between growth and risk of response.
Of course there are things from Civ 1, 2, and 3 I'd like to see in EU .... but that's another thread.