Nor the whole idea of capturing opponents to raise them and make them fight for you. That's from 1987 already, from the Shin Megami Tensei series; it predates Pokemon by a fair bit.
Except they filed a patent for exactly that recently, so I'm guessing it is for the capture mechanics. It shouldn't pass muster in that case, but Japanese courts be wild (and very pro-Nintendo).
I gave it a check. If Pocketpair plays it smart they can make Nintendo look like a herd of muppets in the court, and even potentially acting on bad faith. Pocketpair might also simply change a few elements of its own game through an update, much like PvZ replacing Michael Jackson zombie with a disco zombie.
I'm not even sure how much patents apply to games.