Renting a car is an option for touring Japan in rural areas, where public transportation service is not as convenient as they are in metropolitan areas. On the countryside, trains and buses slide down to a second choice for its less dense networks and infrequency, while cars drop down to a secondary choice in large cities, because of heavy traffic especially in the center part of the city.
There are several Japanese car rental companies, but unfortunately, they do not provide service in English or other foreign languages. You can find counters of the world-wide car rental companies ( such as Avis or Hertz ) at airports and other places, but the rates they offer can not be approved. So for now, I might have to say that discount rates offered by travel agencies, are the best alternative for the time being.
To rent and drive a car in Japan, you must either have a Japanese driving license, or an international driving permit with your home country driving license. As for drivers with driving licenses issued in France, Germany and Switzerland, an official translation of your home country driving license is necessary instead, for the international driving permits issued in these countries are not valid in Japan.
The merit of rent-a-car is that it's good for moving around on your own in rural areas, where public transportation are not as convenient as they are in the cities.
The demerits are that the renting price is higher than they are in other countries, and that local car rental companies do not offer service in foreign languages.