Outside the fact that theological combats are tedious, something that cannot be fixed by patches since it needs a revamp, there are some improvements to make for religion in general.
To begin with fallowers shouldn’t be wiped out by Missionaries and Apostles, those units should decrease the number of fallowers from another religion, but at least one fallower from each religion should remain in the city no matter how many charges you used, also the proselytism promotion needs to go since it wipes out everything therefore is overpowered, particularly if you’re suzerain to Yerevan.
The reason behind the fact that at least one follower from each religion should remain evolves around three points. First because Missionaries/Apostles historically never wiped out entire religion but rather decreased its popularity, so this way the fallowers from another religion would go from being the majority to being the minority, which makes more sense to me, secondly because it would make India’s unique ability more useful, since right now most followers from other religions get wiped out meaning no bonus for India, and last but not the least because if a city as even one follower of a religion this follower may still create some pressure for his religion meaning this religion may still influence other cities, which again makes sense gameplay-wise and historically-wise. Nevertheless Inquisitors could still be able to wipe out all fallowers from other religions in cities within your territory, and in order to balance Inquisitors a little bit, a city which gets a religion wiped out should have a level of negative amenities for few turns in a way to have a possible uprising.
Another issue with religion is the fact that the concept of holy city from CiV is gone, meaning the city where you founded your religion doesn’t get more pressure/defence against other religion. So right now this city is very easy to convert, at this point if all of your cities are also converted it’s religious game over. However if the holy city was harder to convert it might be used as a platform for the religious defender to spam Inquisitors and other religious units.
Moreover I think passive spreading should also be more important, but I don’t have enough experience with the passive spread mechanic to really know how to improve it, even if spreading through trade routes would be nice.