Arceus isn't the god of Pokemon, it's just what a natural Pokemon looks like. The Arcei came to earth years after an apocalyptic war caused a societal collapse and wiped out the animals of the world.
The Arcei decided to repopulate our ecosystems with genetically modified versions of their own species. Embryonic Arcei look like Mew, who is only considered the "ancestor" of Pokemon because the genetic modification begins at this stage of development. The first "true" Mew was merely an Arceus that had been modified to retain it's fetal appearance thru hatching. All other Pokemon are the result of increasingly complex modifications with the intent of creating new animals to fill the ecological niches previously filled by earth species. It is this genetic similarity that all Pokemon share that allows many of them to successfully reproduce across species, though this only creates an offspring of the female's likeness.