Colonial should increase profitability of the colonies at the expense of the colonies - since they're being ruled by fiat, not democratically, their economy is under intense pressure, they're second-class citizens, etc.
Shouldn't increase or decrease rebelliousness (colonies should just -be- rebellious full stop). And it would be great if there was some way that the cities were particularly punishing to the natural environment, in such a way that the idea of multiple colonies - especially from competing civs - is definitely unsustainable. Then that would mechanically underpin the relations hit to other colonial players.
Also while I'm here, I think a core part of an A.I. rule civic should be a penalty (modest) to happiness in all cities. Being ruled over by the xenic otherness of a supermind is unsettling and causes resistance in itself, plus the fact it's not rule by other Humans either. However, if you are plentiful in diversion, luxury, amenities, etc. you would overcome this factor.