When I am asked “which place should I visit in Japan?”, I always ask them in return “Are you a runner?”. If they are runners, I would suggest them to go Imperial palace.
The imperial palace is located at Tokyo Chiyoda and very close to Tokyo station. Tokyo station is one of the oldest and biggest stations in Japan. I believe it is worth visiting. You can get to Imperial palace by walking. You will see full of runners around there. Imperial palace is the place where Japanese emperor lives now and was the place where Edo castle was. It has a spectacular garden, history museum, and a good course to run. It is not too miscellaneous, is it? You can also find the place to change your clothes. Why not running at Imperial palace? You can learn history and see beautiful garden while you are running.
In addition to these, if you are lucky, you can see Japanese emperor. He greets people twice a day from imperial residence. You can listen speech provided by exalted personage, it would be nice if you understand Japanese.