The estimates for Shinto are between 2765 million today. Why is there such a range gap? Because its mostly syncretized with Buddhism and many people are only nominally or nationally Shinto. The number is far less if you're trying to find "pure" Shinto followers. I would argue using contemporary population numbers is also the wrong way to go about it, as a) I view that as a corollary of my "still living" argument, and b) modernity has lead to exponential growth of several cultures yet that increased growth only really has had significance recently and is a poor system for a game that starts in 4000 BC in judging significance on a world stage.
I'll still argue that in terms of numbers, at best you can say that Shinto is equal to Hellenic religion even before AD 380. However, in no way can you argue that Shinto was more significant on the world stage. Particularly Hellenic religion as expressed by Neoplatonic mysticism, whose impact can be seen in the theological beliefs and framework of Christianity, Judaism, and Islam. You can also argue just the mere cultural and aesthetic influence of Hellenic religion in terms of art. There are even forms of Hellenic religion that were monotheistic if that's important to some people.
If we also talking about influence on a world stage, I'm going to bring up Sikhism. I don't mean to offend anyone, but Sikhism is largely limited to one area, and really only began to spread worldwide in the 19th century. Ancient Hellenic religion and Manichaeism had for more impact on world history. You also can't argue it was included because a civ that had a chance of being in the game would use it. Why is it in? Because today it is one of the largest religions in the world. But again, this is today.
I'm not necessarily disagreeing with you, I'm just saying that size and significance, although certainly a factor, was not more of a factor than including living religions.
I'm saying you can certainly make arguments about the "odder" choices out of the 11 (now 13) included religions. You can find religions that were more significant historically than some of the 11. I'd say you can even make an argument in terms of size even if you include modern populations. However, you can't find any larger and/or more significant that are also still practiced today.
And no, I don't care about indigenous religions. For geographic distribution they might be nice, but were never very significant historically nor do they exist today outside of forms syncretic with Christianity or Islam.
I would argue that both a Hellenic religion and Manichaeism should be included with the 11-13 official religions, they can stand on their own in terms of size and impact, and both were certainly more than "just polytheistic or pantheistic religions" as you would say.
I'm also saying that "pantheon" was a poor choice on Firaxis' part as a label for primitive religions, and I think people use the poorly chosen label to discredit valid choices like Hellenic religion. Actually, I think Firaxis might have gotten confused with pantheon and pantheistic as well. As a pantheistic religion would fit with the belief system of giving bonuses to natural land, while a pantheon inherently has nothing to do with that.
The exact same can be said of Christianity or religion in many Western Nations. Although, we could get into a very interesting debate about what it means to be Shinto, as there are some intriguing arguments that can be made on that particular topic. The point remains that there is still a huge number of people who are considered to be Shinto followers.
The issue of using the modern world plagues the game as a whole. The game is massively biased towards the modern world right down to the inclusion of the Shoshone and Iroquois. The religion system already has some vague sense in that regard though, and does offer some historic options for religion, namely Zoroastrianism and Tengriism.
The point about the Hellenic religions is now so watered down that I don't even get what you're trying to get at. Are you now saying that if you amalgamated all Hellenic religions together, and took that total, that it would be larger than the particular set of people that your particular definition fits as Shinto? If so, then we're in for an even longer debate about what defines a religion, what defines Shinto and what gives you the right to declare who are and are not worthy of being counted as adherents. Keep in mind though that the total number of "Hellenic Religious followers" were almost certainly less than 25 million in any case, even in the early 1st millennium. Please keep careful note that I don't see anyone arguing that Shinto was more important, and I in fact was bringing up the the Roman, Greek etc religions as examples of what has been left out as "Pantheon" beliefs within the game. Shinto is a bit of an odd one out though, but due to their size these days (they are within the top 8 religions in the World Today).
I'm not even sure what you're arguing for now, do you want Hellenic religions included as some blob entity? Do you feel that allowing for Pantheon beliefs and having that represent a lot of the religions that would later die out world wide as somehow inappropriate? That is what they seem to have done, whether right or wrong.
You're not wrong about Manichaeism, but they just seem to have gone with other options. While we're talking about Sikhism and Shinto though, I'm curious as to why you've not called Judaism out, which in effect only acted as a precursor religion, and it in and of itself was never all that influential in terms of spread at least on it's own. There have been influential people who are Jewish yes, but at no point was it a major religion in the same way as the others, and in terms of shear number today sits below both Shinto and Sikhism.
As for having Hellenic Religions, having them as a blob would be a bit inappropriate due to the differences between them. Moreover it might be worth noting that the Italy effect might come into play again here. As with the Italian City states and the city state mechanic, here with the Pantheon beliefs almost certainly being largely in reference to the Greek and Roman pantheons, it would seem a bit silly to have them as the base form of that and a major world religion.
Speaking of the differences of Hellenic Religions though, it is worth noting that the Roman Empire was actually quite tolerant with religion. It at it's core followed the Roman pantheon, but as you put it, it was largely Hellenic religions in the "core" region, but varied greatly throughout. No single religion before Christianity really dominated Rome as a whole as such, but rather it was the local beliefs that were allowed to exist, but that's a whole other story and more to do with the complexity of Roman Society than some stickers used as labels in a computer game.