Actually the main line north from Tokyo to Sendai, Morioka and finally to Aomori is pretty flat because much of the line goes along the rather level coast. The Hayabusa Shinkasen “flies” up there in just over 3 hours. The distance is over 350 miles. Remember that the train does have to stop at about 4 stations and wait for passengers to get on and disembark. This “wastes” a lot of time.
If you go over to the west coast from Tokyo to say Niigata, there are many tunnels, curves and elevated sections because you have to go through the “spine” of mountains that runs up and down the country. This Joetsu Shinkasen is fast, but can’t reach the speeds that the Hayabusa can.
When I was in Japan, I used the centrally located city of Gifu as a base. (It also had one of the cheapest youth hostels in the country.) Armed with my Rail Pass, from Gifu I was able to go almost any where in Japan and make it back again by evening. I loved riding on the train. I never tired of the views of the countryside