Any time and expansion comes out, or a major patch, I just to a complete reinstall of the game. I've not had any issues, but maybe it is more ram intensive now than before.
As to the autonomy, I am a conqueror, I love it, I don't always do WCs, in fact I rarely play past the 100 year mark. I am at 1525 in my Byz game and am already thinking of restarting even though it's going really well, I just love the early game. Even by that point, all of Greece, Bulgaria, Serbia, Bosnia, Wallachia, Moldovia, Crimea and down the coast towards Georgia, and the western bit of Anatolia, Caffa, Theodora and a few other places are at 0 unrest and 0 autonomy. I have religious, and tech level 10 on admin, so can convert pretty quickly. I haven't culture converted anything except Kosovo, and that's because I got a mission to do it.
In EU3 it took 50 years (unless you changed it), to get a core on land you conquered and for those 50 years you could suffer rebellions and other nastiness. It takes nowhere near that long now.
I have suffered one revolt, in Crimea when I converted 3 places at the same time with now units there. 3 12-15 stacks popped, they all died pretty easily, and I saw it coming, awash in mil points I decided to see what would happen instead of spending 67 points to reduce the progress by 25%.
I don't see the problem, the progress is even on the side bar and you get notices and everything.
My early game ally Poland with Lithuana suffered mightily to rebels, a new country spawned in Lithuana with cores all over the place, but it only came about because Poland launched some barely win type stacks at the rebels stacks which allowed them to retreat instead of being destroyed and they all retreated to the same place. Only France, Austria or the human player could have beaten the resulting 52 stack of rebels there.
The biggest problem with the AI has been here since the beginning, they generally don't fight rebels until they've successfully taken a province, but under the new autonomy system that's a really bad idea. Unfortunately AI behaviour has not been updated to account for it.
As a human player you have a great advantage, you can design the army to beat almost any AI army, once you understand combat width, flanking, and artillery you will crush the AI, even a 52 stack with your 25 stack in the right conditions.