This is very easy to travel in Japan. Why? Because it is very comfortable. Especially by train. Railway system is developed well and suggested to any traveler the wide choice of train from Shinkansen to rarity trains, which have two cars only. All train are running to time and could be canceled in force major case, earthquake and tsunami for example.
All that is needed in the way, passenger can buy at the station before departing and something on the train. Common level of culture of passengers add the comfort to you trip. Passengers don’t make a noise, don’t talk on the mobile phone at their seats, but go out for it at the special place.
Information in English available somewhere, too.
Please see some photo set, named “On the way. By the train”.