I have a lot of suggestions for American religions.
The first thing is that there should not be any relations modifiers (positive or negative) nor any conversion of provinces between ANY pagan religions, nor should having a different pagan religion present in your empire contribute to negative religious unity. Proselytization and the entire concept of a defined "religion" does not exist in these traditions and is completely misplaced. Yes, people had vague ideas about the neighboring peoples having barbaric ways or whatever, but that does not apply when the religions we are using cover such huge chunks of the map. People in every province of the Aztec Empire thought the next province over were barbarians. Maybe we could add in an option to unlock conversion with religious ideas or some sort of reform path, but it definitely should not be the default.
Okay, with that out of the way, I can get down to individual religions. First, I advocate for making a few entirely new religions: Shamanism (to replace all the animist provinces in the Americas, separating them from Asia), Sacra/Sacraism (to cover everything in the US east of the Rocky Mountains, sacra being a term for religious symbol basically), and Chiminigagua (to cover Ecuador, Colombia and Venezuela outside of the Llanos, potentially also Costa Rica and Panama - this would represent the civilizations of the Isthmo-Colombian area, especially the Muisca). If we ever add Taino nations (which we should, specifically the five chiefdoms of Hispaniola), we should also add Zemi/Zemism, or give them a slightly unique version of Chiminigagua.
Shamanism should get a straight forward system similar to Hinduism, where you pick a certain "spirit" that gives you distinct bonuses. In addition, Shamanist countries will get insane military bonuses for defensive battles in the terrain of their capitals. This is to buff the tribes like Chichimecs, Wayuu, Charrua, Guaranis etc. that were really a significant threat to early colonial societies. I mean, these people were just very in tune with their surrounding environment and were able to use it to their advantage to make it impenetrable to Europeans. If you don't believe me, look up the Chichimec War, or the Guaycuru, or the Guayuu. In addition, this mechanic will reflect nicely that native religions tend to focus attention on sacred places and sacred landscapes as living organisms, really the essence of animistic traditions.
Sacra will have a slider mechanic (really creative, yes I know) between communalism and centralism. Communalism increases slightly every year (due to the Green Corn ceremony) and raises autonomy. Centralism increases with prestige, power projection and low autonomy, and lowers autonomy, reduces coring cost, and increases the number of states available. This might sound a bit OP, and I mainly designed it with Mississippian polities in mind, as I hope that we could see them represented in the game eventually - they would start the game as small chiefdoms, but would have to weather first famines and then later pandemics introduced by Europeans, which would drastically throw the slider towards communalism. Once full communalism is reached, the chiefdom transforms into a tribe. The way to ensure survival of the Mississippian way of life is to build a strong empire. Another quirk is that advisors die when your ruler dies.
Chiminigagua (the name for the supreme god of the Muisca people) will also have a slider, that works a different way, between masculine and feminine (or Sue and Chia). Instead of trying to always concentrate on one side, you want to alternate for the best possible affect to be able to go through cycles of conquest and consolidation. You can perform ceremonies to go either way. Masculine helps you gain prestige and manpower, while feminine reduces coring cost, autonomy, and makes development cheaper. The most interesting part is that the Muisca Confederation was actually split into two rival states, Bacata and Hunza. Bacata was associated with the feminine moon cult and Hunza with the masculine sun cult. Thus, focusing attention on either side too long will increase the influence of that state in the confederation, and could either spell conflict or hegemony.
Zemi would be very similar to Chiminigagua with slightly different effects. Masculine reduces development cost and increases manpower and feminine has split effects: increased trade efficiency/range and naval movement speed during peace, and naval military bonuses during war. This would set any Taino state up for an interesting potential as a thalassocracy. Zemi religion also unlocks the ancestor worship ability, which gives a ruler a chance to increase their MP stats.
Then, for existing religions:
Please, please, please rename Nahuatl and Inti. Please. Nahuatl is a language, in fact it's the language of the Aztecs who make up a minority of the adherents of this religion. It was not even a sacred language or anything. It's the equivalent to calling Catholicism "Italiano". It's so misguided. As for Inti, Inti is one of the many gods of the Andean region. The Incas adopted him as their imperial god and tried to convert everyone else to him. So many other states had alternate gods. It's the equivalent to calling Hinduism "Vishnu".
The names I propose instead are Teotl and Huaca/Huacaism respectively, they are much more inclusive. Teotl is sort of the Mesoamerican concept of god, or rather the spiritual energy moving in all things. Notably Motecuzoma is said to have described the conquistadors as "teotl", by which some think he just meant mysterious or unexplainable but it was interpreted as god. Huacas are Andean spirits or idols, especially those that dwell in landscapes.
I also think that having separate Mayan and Nahuatl/Teotl as separate is not necessary, but I can kind of see it given the doom mechanic (which I actually think should stay). Personally I would just have doom apply to Central Mexican and Purepecha cultures, but it's not that important of a thing and I'm sure the developers like to have it separate for simplicity. But Huastecs should not be counted as Mayan.
For all three religions (Teotl, Mayan and Huacaism), there is something major in common. Choosing a deity to promote as the "imperial cult" and then converting other provinces to that cult, including provinces of any other religion, which retain their own religion, but also worship your deity. Ideally these could even keep track of deities in other religions (including Hinduism, potentially), so that it's easier to convert a province that already worships a sun god from another religion to your own sun god. You can then organize festivals for your deity at a cost of a month's tax income and the trade production of fine goods like silk, dyes, and precious metals, which then increases your "authority" based on how many provinces total in your country worship your deity (not a percentage like religious unity). Increasing your authority is how you access the benefits of your chosen deity. Huacaism has a couple of unique abilities accessed by spending authority, namely mit'a (free point of development in any province) and mitma (a very quick assimilation in culture and religion of any province of the same terrain as your capital). Still working on ideas for authority abilities for Mesoamericans to keep it balanced.
Huacaism also provides administrative benefits to provinces of the same terrain as your capital - easier conversion, lower autonomy, and reduced coring cost. However, for provinces of radically different terrain, the opposites are true. For instance, as the Incas, you would get major benefits to mountain provinces, but major minuses to, say, jungle, desert or glacial provinces. This would reflect both the tendancy of Andean peoples to focus on specific landscapes, and also the unique spread and administrative systems that their empires had.
