It's certainly not Civ6's.
Really I think Civ6's biggest problems in regards to religion are that 1) religion is a zero sum game in more ways than one and 2) religion has negligible impact on diplomacy (a very minor bonus for sharing a religion, a small malus from Philip and a couple others specifically for
not sharing religion). The first could be solved by making beliefs non-mutually exclusive, make religion spread more aggressively via passive means (making multi-religion empires more likely among other effects), and just nixing the religious victory altogether. The second could be solved by allowing empires to declare a state religion (which shouldn't have to be the majority religion in the civ!) and increasing the effect sharing or not sharing a religion has on other civilization. In particular, trying to purge a religion from your territory should
really upset civs that have that religion as their state religion (this was, for example, the motivation for the First Crusade, at least ostensibly). Likewise, declaring a religious war should earn favor with civs that share your religion and bring the ire of civs that share religion with your target. (In general, not just religiously, Civ6 could really use more motivations to create diplomatic blocs.)
Cutting religious victory and increasing passive spread would also help with another problem: historically there have been a lot of religions but only a few have become major religions worldwide (e.g., Christianity and Islam together account for 2/3 of the world's population). By increasing religious spread
and having state religions, this would both increase the number of religions that could be founded while also making it likelier that just a few will come to dominate wide swathes of the world, especially under the consideration that diplomatic pressure will encourage civs to adopt the state religions of their allies or powerful neighbors.
As long as we are in this subject, I always thought that the Religions system in Civ IV was, for some aspects,
way better than Civ V or VI.
For people that don't know or remember, all religions (seven: Christianity, Judaism, Islam, Confucianism, Taoism, Buddhism and Hinduism) were exactly the same: they give only bonuses to culture and happiness. They were founded not by a prophet but when you were the first to discover a certain tech (polytheism for Hinduism, meditation for Buddhism, etc). If you had a large scientific advance, you could be the one that found all religions. You could also choose which religion would be your State religion (because religion had
a lot more diplomatic consequences, especially with Saladin or Isabelle) even if only one of your 40 cities were converted to this. Of course, cities where your State religion was dominant had a happiness bonus, but you could built special buildings of each religion (churches, synagogues, pagodas...) in each city as long as you had at least one follower.
This system was (kind of) organic: religions popped up, you were not really controlling them (you could train missionaries, of course, to spread it the most), holy cities could all be in your empire (when you discovered the tech, you didn't chose where the religion popped) and, with Liberalism, you could even chose to adopt Freedom of Religion.
It was
waaaay better... except for the fact that each religion was the same.
I love the Civs V&VI system of customizable religion. It give flavor, it give depht, in a complete unrealistic way, but it's funnier and more interrestant.
The problem with religion (in Civ VI) is to join the two principles: that each religion has a very specific and unique flavour (like Pantheons, that are more something that "happen" and you don't really control anymore) with the fact that it happened organically.
What could be done is that you allow a number of available Great Prophets equal to the number of AI (12 max). Each civ can earn multiple Great Prophets and, thus, found multiple religions (of course, you'll have to find a way to prevent players to just hoard all Great Prophets and allow only one religion in the world... maybe when a Great Prophet is earned, a religion is automatically founded in the most populous city with a Holy Site in your empire that is not yet a Holy City (if all cities are holy, then just make a city double holy)). Each religion you found, you can choose its tenets and beliefs (as normal). You can have a decision (somewhere) that allows you to chose your state religion. The Religion Victory would not be to make the religion you founded the most important but the owner of the holy city of the predominant religion would win when enough cities would have been converted. This way
could work but I'm not even sure.
But for Humankind, since there will not be a
religious victory
per se, they can handle Religion in a more organic way rather than the Imperial Cult thingy we have in Civ because they prefered to put Religion as one of the victories. So I hope Amplitude will deal the religion issue right (and, IMO, it's not complicated: if you see it ala Civ V, like a culture/happiness producer that have diplomatic influence about neighbor and something you have to deal with rather than control, it will be for me rather good)