Neither. Unless you go chronologically by discovery/creation by gamefreak.
Mew is said to be the ancestor of pokemon. Its a guess, a theory. There has been no evidence indicating any darwinian evolution and besides, Mew looks rather complete and perfect instead of primitive.
Fact: Mew shares DNA with all pokemon.
Theory: It might be an ancestor.
According to legend Arceus is said to have created the universe with thousand arms.
Do you see thousand arms? No. Thats there just to point out how literal this story is meant to be.
It is a myth. Arceus is not a god.
As with the rest of the true legendaries, it is just a powerful and rare pokemon, that lives for ages, and has had people make up local myths about it.
No one outside Sinnoh even knows Arceus, just like Groudon/Kyogre are a myth only famous in Hoenn etc. Why? Because they reside in those places. Ancient people saw their powers and made up creation myths about them, of course always revolving just about their region.. a legend doesn't have to be more than just a story simply because its in a game. In this case, myths are still just myths but the inspiration is an actual magnificent creature.
Fact: Arceus can create a DimensionTrio egg with the help of hundreds of Unown.
Myth: It hatched out of an egg and created the universe with its thousand arms.
Even in the biggest act we witnessed, it merely created a pokemon in a more spiritual way (fittingly as it is a legendary), which is what pokemon can do through normal reproduction anyway, and even for that it needed the mysterious Unown...
So in the end,
neither are factual origin stories, one being a wild assumption, the other being just another local creation myth.
Both pokemon are as exceptional as any other legendary, but not extremely above that either.
The only truth of course is the third explanation. All pokemon were created by game-developers in the image of the real world creatures.