I really like the idea of no stab lose for breaking RMs as Protestants. Other religions could definitely use more too.
With Samsara, do you mean if we had a terrible king, he could become a dog? :blink:
I feel like I should link this (lots of suggestions in the OP). I support the "denomination/strictness" mechanic for Protestantism suggested earlier, and would also like see Fervor replaced with the same mechanic for Reformed.
For Shinto I suggest a "syncretism" mechanic that represents how friendly you are to Buddhist influences from China. max out your syncretism and Budddhism will be considered as "Own" instead of "Heretic" (this could also be used for the Protestant and Reformed with the previously mentioned strictness system).
For Confucianism I'd suggest a system where each new emperor can choose which of the three schools of thought (Confucianism, Buddhism and Daoism) he wants to promote.
For Shamanism, Animism and Totemism I'd suggest a system that shows how these are actually hundreds of different faiths, and how almost all of them were specific to certain cultures. I'd suggest that provinces with an unaccepted culture are considered as heathens even if they have the "same" religion as you. Those who have a different culture but is part of the same culture group are considered heretics instead.