I don't have comments about the economics of Japan's railways, but I was extremely impressed with the system itself:
- The app to direct you through the system was really handy. Enter a starting and ending location, and it told us how to get there perfectly. Over the entire week we were there, we didn't have any issues taking the wrong train.
- You pay by distance traveled by tapping a card when you enter the subway and again when you exit. Different from the systems in the US I've travelled (specifically Chicago) where you tap once at the beginning. Also impressed with how quickly the system read your card.
- The stations where you can make connections are labeled really well with arrows noting where to go next and how far away they are. However those connections can be really long distances. I think the longest was 700ish meters, a little under a half a mile. Seeing 400m on a sign seemed normal.
- Despite the distances between the connections, I don't think we had to transfer more than once ever. The lines were very well related.
- The stations themselves covered a giant area under the ground and had a ton of numbered exits. Take the wrong exit and you could be a long way from where you were trying to go. But we also used the numbers to specify where we were coming from if we were meeting people, and guides used them in directions.
- The trains themselves were impressively quiet. Granted Japan is in general, but these were notably quiet. Kind of a shock to come back to Chicago and hear the secondhand music or people yelling on the phone.
That's all I can think of off the top of my head. Really impressed with Japan in general though. Highly recommended for people to visit.