TheMightyRegulator said:
Word of god states Arceus was recreating the Universe from scratch when he was creating the creation trio for the player in heart gold and silver which is why that trippy moment where scenes that look like they were taken from google were played as clips. I'll have to look for the quote.
Arceus has several feats that place him at even greater than Universal. You don't have to worry about that.
I do see your point though.
Alright, I could also see it as 'starting small and growing to be what it is. I'm just saying it wasn't a robustly created universe, merely a shove. Arceus, therefore, could not, theoretically, destroy everything it created, thus rendering every other pokemon moot. It can, in fact, get its wierd butt handed to it by Mewtwo in a fight.