After living in various parts of Japan for a number of years, I can confidently say that Japan has one of the best (if not, the best) all around transportation systems in the world. The trains are always clean and ridiculously punctual unless there is an unforeseen incident, e.g. suicide.
If the schedule says a train or the shinkansen (bullet train) is leaving at 13:00, it would behoove you to arrive at the station platform well before 13:00, as it will not wait for you even if you’re only 30 seconds late. Often times even an earthquake or heavy snowfall won’t stop Japan’s trains from running on time.
However, it’s not just the trains that are spectacular. Even the buses are clean and timely! Bus stops have real time signs that inform passengers when a bus has left the previous stop and how many minutes remain until arrival. I would say that you definitely get the best value for your money when using Japan’s transit lines.
Lastly, there is nothing that I dislike more than listening to other people’s mobile conversations. Talking on your mobile is absolutely restricted on all public transportation, leaving passengers to enjoy their journey in peace.