I highly doubt pokemon would risk starting a religious debate of this magnitude. they've spent forever trying to keep fanatics off their tails because pokemon metamorphosis is called evolution. its just a term that is used in the game. It means something different there then it does here. Pokemon go through metamorphosis, which is easily seen in the bug pokemon.
larva, cocoon, adult. Caterpie, Metapod, Butterfree.
baby, youth, adult. Charmander, Charmeleon, Charizard.
Humans change as well. I am very different from when I was a baby. Now I don't have wings or anything too crazy, but I have a different number of bones, my appearance is different, and I am physically stronger. the whole evolution debate in pokemon is just people getting stuck on one world.
Also I am a very strongly believing Catholic, so I want to have that out of the way.
When it comes to Arceus I treat it like any other game with gods. Its a piece of fiction which helps explain the game universe. It shouldn't be taken as anything more than that.