It’s a patent lawsuit which might have a better chance than a copyright lawsuit but Nintendo didn’t disclose which patent(s) and Pocketpair also doesn’t know yet either.

You’re right though that any patent Pocketpair is infringing upon would also have likely been infringed by dozens of other games. Nintendo is just upset Pocketpair made millions with a game that appealed to Pokemon fans and want to ensure nobody else does it again.