Personally I have no problem at all with the way religion works in the game. I do, however, recognize that others have concerns, and some thoughts on how they could be addressed. In the doing, we could add some improvements to the game that no-one could possibly object to, I think, and would be welcome to all players (including me).
My view of other people's objections is that they are:
1) Tired of the "fixed" setup, where Buddism is first/easiest, then Hinduism, etc; where Christianity/Islam have an inherent disadvantage to spreading, etc. (This is a gameplay reasoning.)
2) A little bored with the lack of distinction between religions. (This is a gameplay reasoning.)
3) A little concerned that the game has identical effects on society by the different religions. Say, Hinduism is identical in effect to Taoism, which frankly is absurd. We're not talking about the beliefs of those religions, which of course are different, we're talking about the effects on society. (This is a storyline/realism reasoning.)
4) Concerned about the cost of missionaries. (This is a gameplay reasoning.)
5) Concerned about percieved high failure of missionaries. (This is a gameplay reasoning.)
Frankly, I think #4 and #5 they got just right, so I'm not going to suggest any alternatives.
#1-#3 can easily be addressed by two things:
Suggestion One-- allowing the player to choose the name/symbol of the religion when a religion is gained. Gameplay is identical, except instead of "Buddhism", it prompts you to see which one you want.
Suggestion Two-- when you get a religion, you get to choose a benefit from a list of choices. The list will not be mutually exclusive (two religions could choose the same benefit) but the benefits will not be cumulative (if the same civ has two religions which have the same benefit, then that civ only gets x1 not x2). These benefits will replace the Shrine gold bonus. So, you could pick the Shrine gold bonus, and your game will be exactly the same as now. Or, you could pick something else (from the list of half-a-dozen choices) such as,
"Your holy warriors (all units) get +15% strength on attack"
"When at jihad (war), your civ produces military units at +25% production"
"Religion is expansionist and spreads 25% faster"
"Emphasis on family, city population growth requires 25% less food"
Just some thoughts.
Wodan