13 days Japan June - July

I am traveling with my 22 year old son arriving Tokyo. We want to see as much of the country by flight/bullet train/boat/rail that is feasible possible. Does it make sense to book one hotel in Tokyo & use it as launching location. My son studied. Japanese 4 years high school. He is a artist in computer animation, I am a physician. Any festivals to see of course - please.
Thanks

If you want to see as much as possible, then I wouldn't recommend staying in a hotel in Tokyo, but book hotels closer to the area where you want to do sightseeing.

A typical course would be from Tokyo (to Nagoya) to Kyoto to Hiroshima.

In July there's the famous Gion Festival in Kyoto! :)

For a 2 week trip I would stay a week in Tokyo and a week in Osaka. Those 2 locations will be a good base for travelling to other cities. I prefer to base myself in 1 city and travel, maybe do an overnight if it's a long trip (like Osaka-Hiroshima) but keep my original hotel booking and leave luggage there.

From Osaka you can do day trips to Hiroshima, Kyoto, Kobe, Nara, and others.
http://www.japan-guide.com/e/e2157.html

From Tokyo you can do day trips to Nikko, Yokohama, Mt Fuij area and others.
http://www.japan-guide.com/e/e2164.html

thanks for the quick response. I am leaning toward expanding my trip to 16 days

If possible I would like to see Mount Fuji, Kyoto, Osaka Castle, and Kyushu. what would be the best way to accomplish this.

thanks