I was also thinking, why not making the Holy Columbian Confederacy stronger but more instable ? After all, the HCC is supposed to be basically the HRE of AtE, so I say, let's push the logic to the end and strengthen the HCC by making it wider De Jure , but let's make it more instable by adding some mechanic of my favorite mod !
Thoses mechancs are fairly simple and are also present in HiP or CK 2+ I believe, it's a special trait reserved to the Emperor. It can make the position more challenging after a succession, and grant a real utility to the the evangelical religious head (especially if you add the option to claim the throne for a powerfull vassal if he has good relations with the religious head and the current Emperor does not).
I think it's changes everyone can get behind and that doesn't seem too complex to mod