>>3166086Trains will definitely get you to any city of any significance, though the photos you see of rice fields are from a day where I just walked around - it doesn't take long to get out of the city.
Traveling around Japan by train is great - even for the bullet train you can just show up at the station and order a ticket from a kiosk (complete with English interface) and buy a ticket for the next train. No security check-in, etc. On the shinkansen they have a little room for people who need to talk on their phone so they don't bother everyone else (and everyone actually uses it).
