This is a rather interesting little topic. I especially love how this is just like religion, too. You have one side believing Arceus is "God" and another denying such a thing. The latter side is akin to people saying "I won't believe Jesus/Buddah/whatever is God until I see proof!"/"The Bible is manmade and it says that he is God!" In this case, replace "Bible" with "Pokedex". Seriously, now, this is the same argument. It all comes down to faith, really. Ever notice that each region of the "Pokeverse" seems to have its own belief?
Game Freak's pretty clever when you think about it, in putting in that element of faith. Like whether you believe Arceus is God or not, or whether you believe that all Pokemon come from the Cave of Origin (Hoenn's belief), or whether you believe that they come from Tin Tower (Johto's belief), or even whether you believe they come from space (Kanto's, at least in the anime, anyway). The Sinnoh region just seems to be the first to actually outright state that their belief is a religious one, but in a sense they all are.
Has anyone here actually taken a look at Tin Tower? It's very much like the Shintoist temple rituals. And if I recall correctly, the manga adaption of the anime (The Electric Tale of Pikachu, was it?) stated that in ancient times humans believed all Pokemon to be gods. Pretty interesting stuff here. Pokemon's had religion all along, but Diamond and Pearl were the first games in the series that outright confirm it in a sense.