While I don't know Japanese law, and folks are right in US law about prior art, I think everyone is missing the point.
Companies like Nintendo don't have to actually win. They probably created this patent as a throw away to force Pocketpair to waste money fighting it. It costs tons of money to hire an attorney, work through the process, etc. It takes YEARS.
Nintendo probably wants to waste Pocketpair's time and money OR they're trying to get them to just settle and give Nintendo a cut of the profits.
That's how big tech works with tons of patents and how patent trolls keep leeching off society. I have a patent for a button, you have a phone you're making. I say give me 1% of your profit. What's 1% to you? You agree, we don't go to court and the next person that does it I do the same thing, but now I show them how many people agreed and that person is scared and think I have a legit case.
This shit is constantly happening in the background nonstop.
Patent law, copyright law, they are fundamentally broken. But they won't get fixed until something BIG happens.
Nintendo is and always has been a bully. This is just another instance of it.