I would love to see something like this.
The religious wars ideas.
I understand why it is low/no on the list though. It would be hard to do.
That said, I would love to see more boosts/negatives for people who are part of religions.
Something as "simple" as combat bonuses if you are in a region where your religion is the majority religion.
Economic boosts if your lord, and knights, are part of the majority religion.
There are numerous small things that could bring the religion game a bit more into the life and breadth of the full game.