The problem with Crusader Kings game series it's that just like any other paradox game it's a poor simulation and suffers from bad game logic. Series of static modifiers and events acts as gods touch, trying fix the mess caused by bad game logic.
My subjects should be concerned about my power over them, this would calculated differently according to their personality of course but no such thing. Why am I as a temporal caliph, allowed to divorce or disallow my subjects from divorcing to entire sunni realm? Or why Bulgarians and Serbs can't create their autocephalous churches, seperating themselves from Byzantines? Why can't pagans have proper Popedom where the election of pope is inclusive to entirety to their religious realm? Or concerned about popes keep getting elected from same dynasty and fearful of balance of power? Why can't religions have proper authority modifiers?
Like when the religion is weak, you override some religions rules which creates might make it right situation, which was quite the case for both Islam and Christianity. Like Otto I elected pope arbitrarily and elected priests for church lands in his realm unopposed, atleast tried if I remember it right.
Authority of religion and central church institution would simulate the situation early christianity in Britain well for example. Distant peripheries, especially when the central authority (if any) fails to consolidate power should be de facto allowed to do their things. Like celtic christianity meanwhile there was no formal authority of celtic christianity, this is just how we perceive it, it's just power of pope in Rome just failed to reach there, correct me if I'm wrong.
The boons of religion and culture shouldn't be static. I'm Khan of some nomadic steppe land, I conquered enough and I'm ready to settle down. I need to be fed from a greater civilizational aspect, so that the religion and their adherents culture would help me to settle down and build stuff. Merely adopting coptic christianity shouldn't provide me huge boon if the heritage of coptics and their intellectual centres are dead. Same logic for other aspects of course.
The game has no logic, it's series of railroaded static modifiers. It's like Hearts of Iron IV, you finish a focus and boom you get economic boons and half of Czechoslovakia. Of course since there are no better games for dynastic simulation I have to go with CK3. We desperately need competition for dynastic simulation games otherwise paradox and their retarded game engine will continue to release broken mess with a good paint job.