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Arceus isn't god. It can't create and destroy with omnipotent power because it doesn't have that power. It's powerFUL but not infinitely so; it is bound to the same limitations as the rest of us mortals. It can be overpowered, deceived, and killed. Quite easily, in fact, if the movie gives any indication.
What does have that power? Unown do. But every time they are show using that power, they always do it following orders. They are a nameless and mindless collective of infinite potential to create and destroy and they know not good nor evil.
My theory? Arceus is just the thing that used Unown's power first. Through them, it created the Time/Space and Lake trios, and the universe that they and all Pokemon live in. The Pokemon world is the product of the same plot as the third film, but it's Arceus instead of Molly Hale. It is Arceus' dream brought to fruition through Unown's unlimited power. Arceus is not a creator, merely an author, and the Unown are the letters the author uses to express ideas.
It all fits, too:
>Arceus's 1,000 arms
A metaphor for countless Unown doing Arceus' bidding
>Unown existing between dimensions in the tenth film
Because Unown are the fabric that hold everything together
>Everything to do with the Sinjoh Ruins event
We literally see Arceus doing this firsthand!
The only reason I consider it a headcanon and not true canon is because this is just one flavor of the idea. The facts are all here but the exact way they fit together is ambiguous.