Protestant: 11
Shia: 4 (-2)
Hindu: 8 (+1)
ELIMINATED
4. Catholic
5. Reformed
6. Sunni
7. Orthodox
8. Nahuatl
9. Inti
10. Norse
11. Tengri
12. Mayan
13. Ibadi
14. Sikh
15. Coptic
16. Zoroastrian
17. Shinto
18. Jewish
19. Vajrayana
20. Theravada
21. Confucian
22. Mahayana
23. Pagan
First, I want to say, especially militarily, I think Church Aspects are overrated - their bonuses are pretty much the smallest morale and discipline boosts the game deals in. Also, I maintain that, despite their theoretical flexibility, Church Aspects are kinda like Shia piety - it's almost always going to be the same. And once those three aspects are picked, Church Authority is pretty much boring and useless. However, Protestant (and Reformed) get both some sort of mechanics and the general Christian perks (plus they can hold Rome without penalty, and instead for bonus) and don't have a mechanic that automatically makes large European nations automatically better at the religion than both small Europeans and everyone outside of Europe (Euroblobcentrism was largely why I voted against Catholic).
Shia is very militarily (and conversion) powerful... and that's it. It's largely to this elimination as Absolute Monarchy was to the government elimination - a not-actually-that-impressive example of its category that gets a lot of hype from ZOMG MILITARY PERKS.
For now, I'm giving Hindu a nod over Shia because it combines flexibility (with larger per-category bonuses than Protestant offers), some additional MP control, and the ability to tolerate heathens to the point of little-to-no-problem with Humanist and convert enough to keep religious unity within bounds. Honestly, if they let religions other than Christianity and Islam take DOTF (can't even say Abrahamics can take it because Judaism doesn't get DOTF), I might even push for it to take #1.