But if you are living in Japan as a student, with a working holiday visa or any other visa there are 4 reasonable ways to travel around Japan.
The fastest way is by airplane. There are very reasonable Airlines like Jetstar or Vanilla Air. But using low butget airlines can get expensive if you are adding extras like bigger seat or extra luggage. Also flights are mostly limited to a few big cities in Japan.
Day and night bus
The second way is to use one of the reasonable day and night busses of Willerexpress, JR Bus or some other Bus companies. Traveling by bus takes a lot of time and depending on the bus the ride can be very uncomfortable. But if you pay a little bit more, you can get a very good seat for sleeping. Also if you are using a night bus, you can save hotel costs.
Rent a car
Another good way is to rent a car with a big group and split the costs. To travel by car is very convenient especially if you want to go to places which are far away from a train station. The bad side is that prices for highways can get very high.
Seishun 18 Ticket
The last reasonable way is to travel by train with the Seishun 18 Ticket. The ticket allows you to use all JR local trains in Japan for five days. But the ticket is only available three times per year during the school breaks in spring, summer and around New Year.
Last march I´ve decided to go on a journey with a friend by using the Seishun 18 ticket. I chose that ticket because I can´t sleep in a bus and I´m always scared of using an airplane. Also I´m a bit train lover and I thought it would be fun to use many different local trains.
We started our journey early in the morning in Tokyo. The first goal was Himeji. It took us 10 h and we changed 6 times the train to go there. The ride is very long but we never felt boring. Slightly every 2 h we had to change the trains. During the train ride we really enjoyed it to talk a lot or read a book. The time flew by and we arrived Himeji in the evening.
After enjoying the night view of Himeji castle we just went to bed and decided to visit the inside of the castle next morning. Himeji castle is really the most beautiful castle in Japan I have seen so far. The castle is really big and we enjoyed it very much to walk around even it was very crowded.
Besides all the rabbits on the island it is also very interesting to explore the dark side of the island. From 1926-1945 it was used to produce poison gas. Rabbits were used as experimental objects, since rats, dogs or cats are more likely to spread epidemics. Still there are many ruins and warehouse from that time. If you want it is even possible to stay in a hotel on the island.
Bitchu-Takahashi was the last stop of our journey. On the next day we took again the train back to Tokyo. It was really a big adventure for us and we enjoyed it very much.