The Swiss rail network is small but very dense, very punctual, and extremely well designed (the timetable is optimized countrywide across most public transit operators to allow for smooth transfers - it's very rare to require a transfer with more than 15min wait). And it shows in passenger-kilometers stats: about 20% as much as Germany, even though Switzerland is 10% the area and 10% the population of Germany (roughly).

Japan has many things going for it but also some notable issues. The various private operators can be confusing ("oh, your train doesn't leave from platform 4 in this building, it leaves from platform 4 in the Odakyu building"). There is virtually no transit available at night, even within the large metros. Once you leave the main lines the service frequency can be very spotty and the transfers very badly designed. No bike transport even on smaller regional trains (not counting "disassembled in a bike bag" as bike transport).