One of my most liked feature in global strategy games is the dynamic politic, that change countries on the map. I like it in Paradox's games: when some region or colony declares independence, it is very atmospheric. It is not like growing blobs, that cover all the world, but real humankind life. Every country in our world did not only grow, but was divided many times. It is a pity, but Civ series chose the blobing way: you never see new countries, but even that ones, existed at game start, be conquered to middle or end of the game. It is opposite for real modern world, where every empire are fallen apart and former colonies are independent now.

EU4 emulates some part of this process. You can conquer or vassalize someone, but some time they may revolt against you and win. And not only you. It is even more interesting, when AI countries fall not only by conquest, but from inside.

Another very atmospheric part is indirect control of some regions. It is more interesting when you not control every single region you rule, but just guide them and they have their own aims and points. 

I think cultural melting pot is very dependent on these autonomy, independence and other internal frictions aspects. 

Civ 6 tried to model it by loyalty mechanics, but its realization are bad in many cases. Yes, the pressure from others is good idea, but bad idea to make it too abstract. It must be affected not only by size of neighbor cities, but by culture, ideology, quality of life and so on. It is non realistic when a city wants to change suzerain just because 3 cities of another country are near and only 1 of this country. Paradox's way of this is much closer to reality and much more pleasurable.

By the way, indirect ruling also decreases micromanagement, so, it is very good for large empires in game sense. But if micromanagement gives more power than making autonomies and vassals, then it looks like a battle between laziness and might desire. Game mechanics should stimulate autonomies by game rules, not resist to them. It is historical and more fun to play at the same time.