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Arceus is not omnipotent, and used up the majority of its power creating the universe. This is why it can still be battled and caught like a regular Pokemon, and also why we never see it perform any amazing feats of strength. Creating a new Giratina/Dialga/Palkia is impressive, but Arceus can only do it once and merely creates them at level 1. If we venture deep into headcanon territory one can even argue Cyrus knew of these limits on Arceus’ power and decided to go for Dialga/Palkia instead because of them.
tldr arceus is like brahma from hinduism or whatever hes called i skipped a couple of my world religions classes
