Yeah, that was my impression as well. The only advancement in the rules is the sticker(s) you have on your metatype card. The Setup rules just have you set the basic 7 cards in the deck, and I think that's where the challenge level is set--if you keep bought cards from game to game it certainly gets easier.
On the other hand, there's certainly room in the box (and dividers) to separate out individual decks if you want.