Initially I thought I'd quote someone, but rather than just contribute to the noise level of this thread, here's a few words of choice before I go to bed:
1) Anyone who believes classical religion was akin to "natural religion", i.e some "primitive" polytheism, is dead wrong. Through philosophical speculation there was a considerable shift in Greco Roman religious thought throughout antiquity, where a major trend towards "monotheism" - as in one supreme underlying principle operating beyond several minor manifestations (individual gods) - is one of the most discernible and principal developments. That the religion of Homer was not identical to the religion of Emperor Julian or Diocletian is fairly well known, but more importantly, it wasn't even the same as the one embraced by Xenophanes or Plato.
This means that GR was at least as "organized" as some other religions of the game.
2) If Greco Roman religion is supposed to be covered by polytheism/paganism, then why is Hinduism in the game? And if so why isn't polytheism/paganism able to build its own temples and reap the same rewards as Hinduism or other religions? (Hinduism is merely a collective tag for a bundle of pagan beliefs and practices local to the Indian subcontinent.)
3) There are four eastern religions in the game (Hinduism, Buddhism, Taoism and Confucianism) and only three for the rest of the world (Christianity, Judaism and Islam). Does anyone seriously think this makes sense? It's almost impossible to avoid having your knights ride around chanting "Ohmm!" all the time.
4) The notion that only proselyting religions should be considered and therefore GR is out, is absurd on at least two accounts. One: several of the "religions" included in the game are in fact NOT missionary faiths (for example, Hinduism and Judaism) and some aren't even religions at all, but rather philosophical traditions (for example, Confucianism). Two: Greco Roman religion did spread. It spread to everywhere that Greeks and Romans went, that is, by cultural influence.
Clearly, the game's objective is to portray religions with a major cultural impact, that is, constituting dominating spritual factors when encountering alternative traditions. For this, GR and Zoroastrianism definitely qualifies, actually rather more so than some others.
5) Yes, Civilization attempts in some ways to be "historically" themed, but really, it is fundamentally a kind of what-if historical orientation at that. And in terms of what-if scenarios, there is simply no reason other than historical coincidence (Emperor Constantine) that we are christians today rather than followers of say, the Mother Isis. In no way was Christianity more "advanced" than its competitors, in fact there is a lot which could be stated to the contrary.
Another way to put the same thing: If religions were to be geared towards what someone considers major religions today, why on earth are Romans or Incas in the game when it comes to peoples?
To cut the above short, I frankly see no reason why GR and Zoroastrianism were left out of the game, other than possibly design team ignorance. Those two should definitely have been in (and perhaps also some indigenous American religion).
In consequence, this is what I suggest:
1) GR could be included under the name of "Hellenism". That way it covers not only Greek and Roman origins, but includes everything that characterized classical civilization when it comes to sprituality (for example Egyptian or other "oriental" cults).
2) Zoroastrianism should be in, no question about it. Its cultural influence was immense and it's only a minority religion today becuase it was crushed under the dogmatist military machine of Islam.
3) Some "American" religion should be in to give the right flavour to indigenous western hemisphere peoples.
To account for these additions, Confucianism, Taoism and Judaism could be scrapped (in that order). To cover eastern religious forms in general, Buddhism is quite enough since it is ubiquitious, and Hinduism can come along for the ride in order to offer some variety. Judaism might have tremendous covert power in the world today, but it is after all not so much a religion as a definition of an ethnic group, and as far as its religious dimension is concerned, it is of course not only non-missionary, but even actively exclusivist most of the time.
That's all. Thanks.