I like a couple of the ideas for changing how religion is handled in the game.
1. I don't see why religion should be on the tech tree, or the other humanities for that matter.
2. I like the idea of scouts becoming missionaries after a certain number of turns after visiting a holy city.
Back to the first point, why not have two separate trees, one for philosophy, arts, and politics and a separate tree for sciences and technology.Some techs could be available on both trees because of overlapping and some techs on one tree would require a tech from the other tree. The actual religions wouldn't be attached to the religious techs but on a separate kind of tree, which I'll discuss later.
Techs in the Philosophy-Arts-Politics tree would include:
Mysticism, Polytheism, Meditation, Pottery (requires The Wheel from Science-Technology tree), Monotheism, Priesthood, Writing, Monarchy, Literature, Alphabet, Drama, Code of Laws, Theology, Civil Service, Feudalism, Philosophy, Music, Divine Right, Paper, Printing Press, Guilds, Education, Liberalism, Nationalism, Military Tradition, Democracy, Constitution, Economics, Communism, Facism, Radio (Requires Electricity from Science-Technologytree), Mass Media
Science and Technology Tree would include:
Mining, Fishing, The Wheel, Agriculture, Fishing, Hunting, Bronze Working, Masonry, Sailing, Pottery, Animal Husbandry, Archery, Horseback Riding, Iron Working, Metal Casting, Mathematics (requires Writing from the Philosophy-Arts-Politics tree), Compass, Construction, Currency, Calendar, Machinery, Optics, Engineering, Paper (requires Civil Service from Philosophy-Arts-Politics Tree), Banking, Printing Press, Gunpowder, Military Tradition, Astronomy, Economics, Chemistry, Rifling, Replaceable Parts, Corporation, Steel, Scientific Method, Steam Power, Assembly Line, Medicine, Biology, Physics, Artillery, Railroad, Combustion, Fission, Electricity, Industrialism, Refrigeration, Rocketry, Flight, Plastics, Ecology, Genetics, Computes, Satellites, Composites, Fusion, Fiber Optics, Future Technology, Robotics
To obtain techs, currency would be distributed between "researching" for the Science and Technology (beakers) and "studying" for the Philosophy-Arts-Politics tree (some appropriate symbol). Of course the amount of time (ie. currency) that it takes to obtain the techs from the two trees would have to descrease since players would be spliting their allocation of currency between two trees, the religion tree (and later a fourth tree when culture become available through creating music).
I realize that this would be a very large and radical change to the current gaming system that would necessitate a lot of other tweaking of techs, improvements, civics, wonders, etc. Mainly what it would accomplish is the game being a little more logical in terms of real history. This may not be worth the time and effort it would cause.
I also like the idea of having the religions be created on a separate tree and groups around basic concepts or influences on each other. Also good was the specific benefits for each religion so there is some strategy in choosing a religion.
The tieing of actual religions to types of religious practices and beliefs seems very arbitrary to me, as if the creators had to figure out some way to get the religions into the tech tree. After all, (it can be argued depending on your viewpoint) that all the major religions contain elements of mysticism, meditation, code of laws, philosophy, and theology. The only real distinctions are between polytheistic and monotheistic relgions, and that some of the major religions have or haven't used the concept of divine right to select leaders. The whole thing of assigning religions to the techs is pretty inaccurate.
I would be willing to entertain other ways of doing this . Primarily, it might be worth considering yet another tech tree for religion. In this tree the religions would be organized into logical groups based on core beliefs or historical relationships between them. You could have Paganism (Animism, Pantheism, Totemism) leading to Polytheism (Pantheonism and Hinduism) or Eastern Religions (Buddism, Taoism, Confusinism) or Monotheism (Judism, Christianity, Islam). Each religion would have its own benefits which would be logically appropriate to that religion. There would be an equvalent beaker-like cost to move from Paganism to any of the three other religious groups. Within each group you could choose which religion you want to adopt based on which benefits were best for your civ. Again, the building, wonders, and civics and such would have to be tweaked to accommodate this change.
I personally don't like the race to found religions, treating it like it is an arms race or space race because there should be no distinct advantage to one religion as being better than another. So why race? Instead pick the groupings of religions which best serve your overall strategy for the game. Each grouping could appeal to different styles of play based on what benefits each grouping contained. If you were interested in more historical accuracy, you could choose the religious package that was historically accurate for your leader's culture. It always seemed very strange to me to be playing, for instance, Louis XIV and found Hinduism.
If you wanted to keep holy cities in the game, a player could select a holy city for his religion when he adopts a religion and move it when he switches religions within his chosen grouping of religions. Holy cities would act the same with the exception of their effect on converting units to missionaries as discussed above.
With this system, religion would still be an intregral part of the game, but it wouldn't be as competitive. The counter-balance would be that it could be more historically accurate if a play chose a religion with that in mind.
Sorry for this post being so long, but it is a big subject and a big proposed change.