Not only state of art trains are running in Japan. Of course there are plenty of old fashion trains are running especially outside of metropolitan areas.
Usually these trains are first introduced to metropolitan areas and then transfered to rural areas after the metropolitan areas introduced new trains. However, the trains must be modified to run in rural areas before its operations.
For example, trains in metropolitan areas have at least 3 doors on the each side of the train, sometimes 5 doors and train composition is at least 6 cars. Then, the seats are usually long seats which is pararel to the windows. However, trains running outside of metropolitan areas have 3 or less doors and maximum train composition is 3 cars. Then, people do not prefer long seat pararel to the window but prefer sitting in the direction of the train.
If you are going to Japan and want to enjoy taking trains, definitely should take local trains where you can meet more local people.