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).
This also somewhat prevent having unified ticketing systems like you have in Switzerland.
The ticket you can buy in the train station is also valid for the local buses. Or even better (from a practicality point of view), you can use an app that track your start and end point and automatically bill you accordingly (you rare have to stamp your ticket when using public transport; you just come and go and there's sometime controls by agents).
I'm sure that there's some exception in Japan, like JR West, Central and East are technically different companies but the tourist JR pass allows you to go wherever, but it's hard to beat the convenience of the Swiss transports.
True, although you have to periodically remember to top up you account (my last trip to Japan was short in duration so it wasn't worth it to get one; my memory is probably biased)
My experience, having traveled a lot, is that even those countries/municipalities with good public transit are still pretty confusing for visitors who aren't familiar with the system/haven't downloaded the right apps etc./are jet-lagged/don't speak the language. Some usability testing would really be welcome.
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).