Generally if you take province that are the same religion you are maybe...30ish years until the are at 0-0, same culture, a bit more quickly, and you can accelerate it by paying attention and using those buttons, those give you a 30 year bonus one way or the other. If you have lots of military points, just let the rebellions grow and crush them with Harsh Treatment, autonomy will drop and as nationalism fades away, the revolt risk drops to 0 and Autonomy drops at, depending on government type, and how often you are at war, 1.2 per year minimum. It's really not bad, I have conquered a lot in my Byz games, annexed vassals suffer the same issues, but they are much better 20 years later, and 30 fully productive. It's a bit closer to EU3 in that regard.
