After Fuji, we went to the land of countless temples and shrines, Kyoto, also the former capital of Japan. The people in Kyoto said, "Even if you visit a temple/shrine a day in Kyoto, you still cannot finish all the temples/shrines in a year". This is true because there are over thousands of temples/shrines in Kyoto itself.
The most efficient and comfortable way to get from Fuji to Kyoto is to take a Shinkansen also known as the Bullet Train. It was my first time trying out Shinkansen and the experience was great. Personally I would prefer Shinkansen over domestic flight.