This thread has tons of good ideas in it. Thinking about many of them made me come up with my own ideas that could add a lot of fun (or possibly frustration

) to the game and make spreading and obtaining religions more interesting, challenging and lower the initial randomness, perhaps good, perhaps bad, depends on your point of view.
1. Lower dramatically the chance of random religion spreading, Holy City Wonder can increase it to it's base chance as it currently stands after founding a religion! Disciples are otherwise for the most part required to spread religion effectively. The Primary benefit of being the Religions founder is therefore time to dominate your religion by building it up, should you choose to pursue that path. And of course one city starts with the religion as well as perhaps a second disciple so you can start off with 2 cities of the religion you found.
2. Philosophy enables access to build 1 World Ritual per religion (as suggested by someone else in this thread). Building a Ritual shows the city it is created in to all civs (under FOW of course), this is to give every civ a Pilgrimage marker so they know where to go should they decide to wrest knowledge of that religion for their own benefits. Any of these rituals additionally enables the creation of the "Pilgrim" unit to all Civs (using Manhattan Project mechanics) and possibly creates a Religion Specific resource on a free tile in the cities fat cross, whose only purpose and bonus is to transform visiting Pilgrims/Prophet's into a Disciple of it's type.
*Note the Prophet can be used to duplicate the purpose of the pilgrim, I'm not sure if technical limitations however would require a separate unit, as hidden nationality promotion could be a viable way to get through hostile borders, albeit making it even riskier, that would otherwise be impossible to negotiate open borders with, and I'm not sure if requiring diplomatic relations is part of the challenge and fun that I'm aiming for with this idea, although it certainly would add diplomatic necessities, it could add some interesting options to this whole thing as well which may be worth having in addition to this "pilgrimage".
a) Ritual of Leaves - cost 1,000 hammers, spreads leaves to city, duplicates as Temple of Leaves. Turns Pilgrims into Disciple of Leaves.
b) Ritual of Kilmorph - cost 1,000 hammers, spreads runes to city, duplicates as Temple of Kilmorph. Turns Pilgrims into Disciples of Kilmorph.
c) Ritual of the Deep - cost 1,000 hammers, spreads OO, duplicates as OO Temple. Turns Pilgrims into Zealots, at least I got one disciple's units name right

d) Ritual of Order - cost 10,000 hammers, spreads Order, duplicates as Order Temple. Turns Pilgrims into Disciples of the Order.
e) Ritual of the Veil - cost 10,000 hammers, spreads Veil, duplicates as Veil Temple. Turns Pilgrims into Disciples of the Veil.
f) The base temple enabled by Philosophy is required to build the "Pilgrim" units enabled by each of the rituals. I think 1 unit can cover all the religions it only matters which Ritual city site, they make a pilgrimage to as to what type of Disciple they'll become.
The Order and The Veil Rituals may actually need to be pushed back to some other tech to prevent an AI from foolishly starting those Rituals when it only has 1 city and 10 hammers in production, meaning it basically cripples itself to build it...which some silly AI may very well do.
Each religions Holy City Wonder can be built in any city just like any other wonder, but requires you to follow that religion to build it. No more having multiple Holy Cities & their Wonders under your control, gaining the huge benefits of all of them while running whatever you want as a state religion. Of course you can switch quickly and use GP's or GE's and then switch back but that will come at the cost of turns of anarchy and the limitations placed on civic changes minimum of 10 turns even for Religious civs. Hopefully it's also possible to only provide the benefits such a wonder offers while running the required state religion? Which means there is no reason to have multiple Holy City Wonders, just your prefered Religions one!
Of course this would all be very difficult for AI's to understand and make use of, but they already barely make use of religion if they don't found their favored religion, so I think the loss would only be marginal, not to mention with these changes hoarding religions as a player is wont to do is likely to not make sense in the long run as the cost would be too great, which means AI civs are more likely to be the founders of the civs they like and then spread them to their friendly neighbors the way they usually do.
I think Pilgrimages would definately add some real flavor to the world of religions. In this way you can also make the techs that enable all the benefits of your chosen religion much cheaper to learn but also require it's state religion to learn seeing as the initial work of discovering religions is based on hammers, which are also refundable in gold (runner up prize) when losing the race to the ritual of choice. While still allowing players to actively go get their religion of choice asap and if they're fast enough with stealing the religion from the founder they can can still possibly gain all the higher tier Religious benefits which currently default to the founder that doesn't need to work beyond the initial tech race.
This way also makes the rituals expensive enough to prevent someone from hoarding religions by having them come about early enough that the hammer cost is prohibitive, while if players do manage to build a 2nd or 3rd Ritual then they actively have the means to prevent it's spread to some small degree, which is generally the purpose of founding 2 or 3 religions, without enabling overly easy access to the benefits and penalties of multiple religions (quite frankly in FFH2 the benefits of multiple religions still far outweigh the drawbacks, unless you want really really huge 30+ size cities).