There are also cheaper passes that are region specific or route specific.
There are also cheaper passes that are region specific or route specific. The Hokuriku Arch Pass might work well for you as it goes via the quieter Sea of Japan side and is a bit cheaper than the full Japan Rail Pass while still covering the two main destinations of Tokyo and Kyoto. This one is excellent value for Kansai, the region around Osaka/Kyoto/Nara, for example.