Hmm, I foresee lots of complaints about the way religion works, and lots of PC screaming going on as well. Maybe in civ 5, it will work like this:
(1) Religions have generic, made-up names, so as not to offend followers of actual religious beliefs.
(2) The way your civilization develops determines the nature of the religion long-term. By this I mean:
If a society has to fight many wars, its priests become fanatical, preaching fire and brimstone to the followers. Military units have a chance to convert citizens in conquered cities.
If a civilization has a chance to follow a peaceful path, its religion focuses on the mystical. Cultural buildings become a bit cheaper, and science flourishes due to the many educational institutions founded to reflect upon and study the nature of the world.
If a formerly strong civ that founded a religion goes up against the ropes, the religious practices change. Followers in conquered cities may become fanatics, and take up arms against the city (partisan units outside the walls). Or, they may follow a pacifist path to resistance, refusing to work tiles or pay taxes.
(3) There are no missionary units. Your citizens may have a chance to convert to a specific religion based on trade routes with your civ. Proximity also matters. Citizens in border cities may become enamored of a different religion in a neighboring civ and convert. Even wars would be a factor; exchange of ideas through contact with alien civilians and soldiers might bring about new converts.
(4) Religion makes a difference to your citizens in a way that nationality cannot. If 2 other civs are at war, and you are friendly with both, atrocities perpetrated on other cities makes your own citizens of the same religion unhappy. They may protest and agitate for war.
(5) Since you may have multiple religions in one city, it is possible to build multiple religious temples. churches, etc. The more citizens you have of one particular religion, the cheaper the religious structure is to build, up to a point.
(6) Occasionally, religious strife may occur in a city. Two opposing factions clash with one another. There is the possibility of religious buildings being destroyed, riots, citizens unwilling to work tiles, etc. Military force may quell the fighters, and it may be necessary to expel some citizens from the city.
(7) Finally, in the Modern Age, organized religions can exert political influence. If you are following a peaceful path, with most citizens being in a pacifist religion, you may find it impossible to build nukes in a city because many citizens walk off the job. You may find yourself unable to get out of a war if the followers of an aggressive religion are in the majority; when you try to make peace in the diplo screen, you find that you cannot.