What complete & total hogwash. You get a Great Prophet (by building Temples & Sacred Sites), & you use said Prophet to found a religion....oh my God, its all so very, very HARD (SARCASM). Compared to the new combat system, the religion system I'm suggesting is actually incredibly *easy*. Unfortunately, the game designers seem more keen on building a complex war-game than they are on building an interesting & well-rounded representation of history.
So far you've suggested:
-Using some sort of system to buy religion, either via culture or another piety counter
-A completely new AI layer to monitor religious activity
-A new city attribute, religion slots, that the player must keep track of
-Scaling religion bonuses with the amount of a religion in a city
-City-states intelligently handling religion in diplomacy
And this all gets rolled into one big new system for the game to handle.
None of these are easy or simple by any stretch of the imagination. Compare against the new combat:
-1upt
-Units that can fire over other units
-Hexagonal tiles
-Enhanced military AI that can handle the tactical difficulty of 1upt
Notice how the war aspect of the game was completely revolutionized by three mechanical changes, adding depth without complexity, and one necessary coding one. Religion can't be fixed like that; it would need something like you're suggesting, where you're adding so many mechanics/tweaks/systems that it would overwhelm the player's attention. Ultimately, that's not very fun for the player, as it draws the player away from the richness of the rest of Civ and into the minutiae of the religion system.
In short, from what I can tell from design and interviews, the mantra behind Civ5 seems to be "depth through simplicity." For better or for worse, there's no place for religion in that kind of design philosophy.