I have a few thoughts about religions that I want to share with you.
First of all I strongly support the idea to make certain religions foundable by certain civs. This can be done like in EE3.
Now, my main problem is, that the early religions become dominant too easily. Aesir is only 2 techs from the start for example. In my current game 7(!) civs have Aesir as state religion, 3 or 4 Mesopotamian, 2 greek and the rest is me or destroyed. I founded 3 religions as Rome: 1st Egyptian it spread quite well, as there were still a few "empty" cities. The other 2 is Zoroastrianism and Christianity. Z has spread to only 1 city naturally, the other was by the missionary I got on foundation. C spread only to Rome and only by missionary. I also noticed when I sieged one city after the other that they were also stacked with missionaries. The AI, especially the ones with Holy Cities use missionaries very actively. In my other game the schythians were busy converting my christian people back to druidism. (I didn't cancel the Open Borders because they were one of the few who were willing to trade with me.) It's good to see that the AI finally uses the religious units, but it makes the spread of the late and should-be-powerful religions (christianity, zoroastrianism) impossible.
I thought of two possible solutions.
1. Strip the missionary from the early religions and let them spread only naturally. This may seem drastic,, but think about it. These religions established in certain geographic regions, and that's it. They did not expand but co-existed with many other religions, brought by conquerors. For example the greeks tried to spread their religions in the hellenic states after Alexander, but the influence of the local religions, mystic cults was stronger, so the conquerors assimilated: it was impossible to make a classical greek or a roman believe that his king=a god, but that's what the Ptolemaios and Seleucid dynasty did. This method would (hopefully) make the early religions "obsolete" over time, but that exactly what happened. It's hard to imagine a druid coming to town, banging everyones head to worship nature
2. The above solution presents some gameplay balance issues and maybe it's too drastic. The compromise is to make all missionaries available with the late religions. Like Theology or something. And perhaps cut back the spread rate of early religions. This way there may be space for new religions to spread.
(3.) Another solution, but I don't think it's possible, is to make certain religions (for eyample: egyptian, mesopotamian) spread only within a certain radius. That would stop cities converting to your religion on the other side of the world without having any contact with your civ (as it happened with me and a phoenician city: that was my first contact with that civ) I guess it is impossible because of the engine but perhaps you may enlighten me about that.
I hope I was helpful and constructive and most of all clear. Sometimes I feel if I was just rambling about