1) Empire Blobs
At the moment I have a game where the HRE have included France and Aquitaine to its list ever since the game started, and it never seems to fall either. Similarly the Byzantines stretch from the Adriatic all the way across the Euroasiatic steppes. The Abbasids and Umayyads have been dealt with due to Decadence mechanics and similar so the middle east is barely an issue, but the Christian realms are way too stable.
2) Culture
Previously mentioned HRE is mostly based around the French rather than the German, thus the French culture stretches into parts of Germany. So far so good. Now there've started turning up weird French enclaves in the Carpathians, Pommerania, southern Italy, Africa... it really grinds my gears, I'll tell you what!
3) The AI
Now I know this is a very major part of the game I complain about, but I stand by it! I mean most of my arguments above would be dealt with if the AI were just thinking a bit more like a Meta-Player and a bit less like a randomized unit. If the German lords cared a bit more about staying German, if the Bohemian peasants cared a little less about their lord being French, and so forth. If they just could have some sense of self-preservation y'know?
4) Peasant Rebellions
I mean as it stands the peasants trying to deal with the above French lords on their territory would have no shot, since the 40K+ troops of the Kaiser would take care of them without blinking. At the same time had it been only local the some times 4k peasants would steamroll over any province they tried to take. I don't know if I have a good suggestion for this, I only know I see this as somewhat of a problem.
X) Tanistry
My vassals keep voting for worthless people with below 10 in all stats and horrible traits they'll hate rather than the more awesome 11+ in all stats guys who're brave and just... what am I even supposed to do with that?