The rental car segment in Japan is really tiny - perhaps this explains the high prices. I would hazard a guess that fewer than 0.1% of tourist arrivals opt for car rental at any point during their journey. I did last year, and I am glad as it enabled me to see Japan's wonderful mountainous interior - from the area around Nikko to Shirakawa-go and the Kiso Valley. However if you want to be in urban areas there really isn't a need for a car (with the exception perhaps of Kyoto where you might save a few bob compared to going round by taxi everywhere).