I think it has to do with the lore of the legendaries.
Platinum plot spoilers:
I do agree that it does kind of show that the writers were trying to outdo each other, and that Arceus wasn’t as strong as it should have been, but I think the story was incredible, and that it was more about just being able to catch the Pokémon that created the universe, and less about being able to create the universe.
so, yes, there are some problems, but those aren’t really main features. (And, as far as I know, you can’t get Arceus at all anymore, because they disabled internet features in 2014, which still makes me mad.)
Edit: also, what if it’s not coming with you, you’re going with it? I mean, it created the universe, is it such a stretch that it could create a human that would catch it and journey with it?
(Just a product of my tired mind, I think)