It seems to me that there is way too much money in the game. In one game starting in 1066 it was about the year 1180/1200, i conquered the duchy of estonia to give it the teutonic order. When I checked the newly conquered land, the cities already had built a small university and generally were already maxed out, waiting for better tech to further upgrade their buildings. A pagan university in 1180?
Also heresies absolutely destroy nations. In one game the French queen turned heretic, which meant " holy war free for all", i took Flanders and turned it into a republic= cashcow. In another game the HRE selfcombusted because the emperor turned heretic. Could you make it so that whenever a Ruler turns heretic, his vassals try to depose him (the not- de jure vassals breaking off is okay by me). The heretic holy war for outsiders seems overpowered as well. Certainly when a ruler turns heretic, other nations should be able to interfere. But again but it should only be to topple the existing ruler and replace him with non-heretic ruler.