Hmm. Well, it has always seemed to me that religion has kind of been phased out by modern progress in the Pokémon world. Obviously not entirely, as there are still religious buildings like the church/Foreign Building (Suggestive of a non-native religion? But then why have a stained-glass mural of Mt. Coronet?) in Hearthome, and the people in there seemed to worship the relationship between people and Pokémon. But on the whole, I have always gotten the impression that the Pokémon world's society has become so technological and science-based that religion has sort of faded into the background, although the general populace still appears to respect most cultural beliefs and sacred constructs, like Snowpoint Temple and the Ruins of Alph. However, most of what we see or hear that would indicate a religion usually comes from elderly people, or from people who study myths. Or the Draconids, who are a secretive cult.As you said, Arceus and Rayquaza do have modern worshipers (some few people in Johto who carry on the traditions of the Sinjoh clan, and the Draconids, respectively), but in the wider scheme of things, they don't garner much recognition. Rayquaza is barely ever seen anyway, so not many people even know that it exists, and similarly, Arceus has faded into obscurity so bad that not even Sinnoh natives who know of it can tell you what its actual name is.
Most people seem to regard Legendary Pokémon (particularly the A-listers; i.e. most of the ones that are banned from Battle Facilities) as mere myths, if they have even heard of those myths. But then there are ones such as Tornadus, Cresselia, Heatran, and even Xerneas/Yveltal, which some people have actually seen for themselves or have legitimate historical records of, but few think of them as being anything more than remarkably powerful Pokémon.
Don't ask me about things like the Punk Girl in Kiloude who gives you the DNA Splicers or the Hiker/Street Thug looking for a Genesect; I just don't know.
but Team Aqua mentions Poseidon meaning that at some point in time, some people in the Pokemon world believed in that Pantheon.
Really? Wow, that's very interesting. I wonder what their version of Poseidon (and, presumably, the rest of that pantheon) is like; are they comparable to ours, or do they have their own spin on it? I highly doubt that we will ever get an answer, but that is fantastic food for thought.
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