Japan has the most developed and complex public transport systems I have ever seen, even more sophisticated than Hong Kong, New York, or Seoul. Unfortunately, despite the sophistication, the lines are not very well integrated, with multiple transport networks in each city, each with confusing mutually incompatible fare systems.
Shown in the picture in the background is the Japan Rail (JR) timetable flipped to the page with the Shinkansen schedules and the Tokyo subwap map (yikes!). Overlaid on top are the Tokyo and Kyoto subway passes and the Japan Rail Pass which allowed us (almost) unlimited rides on the respective lines during our trip.
most informative article you ever posted.