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Pokemon are similar to Kami in nature. You have lesser beings and higher beings, with varying degrees of supernatural power. Just as, say, Totoro is on a scale lower than Amaterasu, Snorlax is on a scale lower than Arceus both in terms of lore and game mechanics. Or say, Jack Frost and Beelzebub.
Yes, Arceus is a deity figure. So are Dialga, Palkia, Giratina, the actual Kami trio, and so on.
