While the primary goal of the game is to get all of the pals, most of your time is spent putting your pals to work building up your base, breeding better pals, and manufacturing the weapons needed in order to get even better pals. This is a stark contrast to Pokemon games, where you just walk around challenging gym leaders. It's an entirely different game.
So if Pocketpair reskinned a few assets sure, pay Nintendo 5% at most. But those skins had nothing to do with the success of the game and Nintendo doesn't deserve anything more than that.