I cannot say that summer is the best season to visit Japan. It’s very hot and very humid. But it’s vacation season anyway. School summer break kick off on July 20 in most of area. And mid August is called “Obon”. It is one of the busiest period in the year. If you travel in this period, train may be booked out quickly. Please see the details in the link below:
Japan Rail Pass, many rail passes and rail travel in Japan complete guide. Let's use the Japan Rail Pass to its maximum!!!
Many train lines are closed in Takayama, Okayama, Hiroshima and Shikoku due to serious damage by heavy rain storm in early July, 2018. Please check Train Operation Status to get the details.