Springtime probably just pips Autumn to top place as the best season for Cycling in Japan but this is largely due to the popularity of the Sakura. However, the temperatures and comfort levels are pretty similar for both seasons.  For those planning long tours, as a general rule if you are starting in the early Spring then start south and head north; and for those planning to ride in early Autumn, start north and head south. More insights into the best season for cycling in Japan here.