I suggest this mechanic because it can make game interesting.

I suggest autonomy treaty (can be for some turns or permanent) in which minor civ will become part of our empire but we have no control on city growth, policy and population distribution but is controlled by AI acting as autonomous goverment. 

Keeping people happy should be focused if we fail to do so (it usually occur when you try to remove autonomy that is gaining total control or policy or warmongering or influenced by other)

The AI of autonomous territory can ask other  civ for help and start forming hostile troops in our territory and fight war against empire and gain independence.

City of your territory can ask autonomy if there is high unhappiness.

Autonomus govt have there trade menu and we can give gold or cancel autonomous treaty. While cancelling treaty we get 2 options for give independence or remove autonomous government.

If we choose remove autonomous govt. then it spawn troops and we have to capture all territories to integrate it. 

This can give civil war scenario.

Capital city cannot gain autonomy