I'm in the same predicament. I'm taking my son next October. We will be flying into HIJ then take seven days working our way back to Tokyo, where we'll stay a week. I'm thinking 2 days in Hiroshima to see the city and Miyajima. Then perhaps 3 days based in Kyoto to see Kyoto, Nara, the Yamazaki Distillery, and who know what else. I then want to do 2 days to see Fuji and Kamakura.
I think I will make reservations for Hiroshima and Kyoto, but what about Fuji and Kamakura? I'd like to have flexibility and committing to set reservations will prevent us from spontaneously deciding to route ourselves along the northern coast of Western Honshu, which has peaked my curiosity.
Given the hopefully low tourist season in October, do we really need to have set reservations everywhere?