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.
It’s crazy that they released it. They had early access and preorders and those only attracted something like 1,000 players. This is a game that had a $100 million budget. So few players during the early stages should have told the studio to cancel it while it was still in production. Apparently they thought they’d release it and would just jump from 1,000 players to 100,000 overnight with no changes.