Haven't read the thread yet so I'm not sure what people have said.
Overall I like the system, it is pretty great, works better than IV or V IMO, obviously there are some balancing issues such as Adam Smith but that's to be expected with a still relatively new game. But there are two main things I would change.
One, as people have pointed out some GPs especially late game GAs are relatively useless. Why not solve this problem by bringing back one of the pretty good features from older civs that's gone now, Golden Ages? Do it like Civ IV, 1 GP of any type can start your first GA, after that you need 2 GPs of different types. Gives you something to do with useless late game artists/scientists, adds an extra decision with the less awesome ones of do I want to use the ability or save for a golden age?
Two, and this really just seems like an oversight that jumped out at me the first time I played, why are Great Prophets not in the game at all besides founding a religion??? There just seems like 0 reason for this given the rest of the system, it would make so much more sense to just have the first 6 (or whatever) Great Prophets found a religion, and after that they continue to exist and provide bonuses. You could have ancient ones that evangelize beliefs, ones that add bonuses to your Holy Site buildings, build a free shrine/temple, spawn missionaries/apostles/inquisitors, or add a buff to your missionaries. Or just don't bother with any flavor at all and have them just act as a super-apostle with 5 or 6 spreads and 120 religious combat strength, anything is better than just not having them in the game, period. It makes the Holy Site buildings even more useless outside of a Faith game by taking away their GPP, and adding minor boosts to religion through prophets would help it contribute to the rest of the game. And if you have nothing to do with one or spawn one with no religion, just start a Golden Age lol.
I can see not wanting prophets in the late game but just cap them off at 1-2 per era post industrial or shut them off completely at that point, the game is already well equipped to handle running through the GP pool. There's just no reason to have no prophets after 2000BC, the feature is already in the game it's just been left out or overlooked.