I think the independent people feature need work because they have not that good impact on gameplay because they are very weak feature because:

Assimilation should be difficult

The feature which show decline or young settlement or stable should be removed

They can be easily defeated

They cannot survive in later eras

They can impact our gameplay like can't give bonus like science boost or economy or cultural support

The changes can be done like 

They can have a role or speciality which i can only get if having  good diplomacy, trade, war support, special unit, etc.

Independent people should also have diplomacy.

In later eras independent people can form from revolution start capturing some cities and outposts.

 There can be scenario like huge empires collapse and many independent states forms.

Revolution can be of types which will form independent people of following types like:

Having city on another continent cause revolution for anti colonization revolt, the independent people try to capture territory on that continent. This can be stoppable in diplomacy by having peace deal. 

If you capture or assimilate previous existing independent people territory the revolution can be fight for freedom in which they will try to capture there old territory.

Please share your views