Arceus made the pokemon and all that stuff, thus he's not the ancestor, he's the creator. Mew would have been theorized as the first pokemon on the planet and populated the world with it's kin, all of which would have over time evolved into the various species we see today. This makes Mew the Ancestor.
A religious way to put it is this... Is god the ancestor of all people? Wouldn't that be Adam/Eve?