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Mewtwo still isn't even close to being the strongest lore-wise, and it's implied what we see of Arceus isn't its true form.
Base stat dick waving means nothing in the face of the entity that created the rules which allow those base stats to exist and have meaning in the first place. If Arceus doesn't feel like tweaking things to make the Mega Mewtwos as impotent as a Magikarp, then it can just use timehax to Judgment the Pokemon Mansion before Mewtwo's development even began.
