(Posting from my cell phone tonight.)
There are a few different ways to get around Japan.
First, you can walk or ride a bike. These work well for short distances with little to no luggage.
After that there are cars, trains, and buses. Each of these are about the same as in the western world (just cleaner and better).
For longer distances, you usually go with either the shinkansen, regular trains, buses, or planes. Planes are the fastest, but also the most expensive. The shinkansen can cost almost as much as a plane and isn't as fast, but it's nice in its own way.
Buses and trains, for the long haul, offer the night (夜行) option. Basically, you get on the train/bus in the evening, and wake up at your destination. It might not be as glamorous as the other options, but it is a little bit cheaper.
I took the night train from Kyoto to Akita back in 2001-2002. It was really neat, and the JR yukata (robe) that followed me home is still a prized possession.
The night bus, though, ain't all that. Just like everywhere else, the seats are too small. The rocking of the bus is less "gentle and soothing" and more "gee, I'm on a bus".
Not much I can do about it now, though, except have a drink and try to sleep.
Good night.
