Unique inn, small changes would improve experience
Having said that, there were a couple things that could be improved:
1. There were some extra (I would almost say hidden) fees; firstly, the price we were quoted for dinner did not include tax, but secondly (and this was more annoying), after we booked we discovered that bringing alcoholic drinks to the room would incur an expensive per item fee unless we bought a bottle of wine from the hotel as well (which we personally thought were overpriced for the quality). We've stayed in many hotels across Japan and never encountered such a rule; after all, this is a hotel, not a restaurant! In the end, because we did not want to pay to bring our own drinks or order any of the wines offered, we just drank water. Nothing wrong with the hotel offering drinks, but guests should not be charged for bringing their own.
2. The futons were too thin; my wife and I both had backaches by morning. They could use one more layer. Also, unlike most Japanese inns, the staff did not set up the futons. While not a big deal, considering the cost of our stay, I believe the staff should set out futons for guests.
Again, this is a unique inn and better than most, but small changes would make it even better.