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Arceus isn't actually God in all of its power. It's more like a christ figure, or a sacred animal. It's very powerful, but it isn't omniscient and omnipotent like the actual creator of the universe. It's a fraction of what we'll call the "real" Arceus, which is why the player can catch it, and why it can be KO'd with conventional battle. This would also why it talks of Arceus creating the universe with its thousand arms, yet its Pokemon form has no arms at all.
