Many people who've never been to Japan before probably have a picture in their head of what Japan is like, maybe due to pictures, movies, whatever. Maybe they picture a sprawling metropolis full of people, neon lights, cute characters on anything and everything, a silhouette of Mt. Fuji, shinto shrines, moss covered Japanese gardens and painful-looking gameshows (which are pretty awesome btw). Don't get me wrong, these things do exist here...but in maybe only 25% of the country. The rest is what you would call the inaka, rural Japan.

Town of Engaru, about 10 minutes away. Population 23,000.
The rest of the country consists of rice paddies, wheat fields, onion fields and whatever else they grow (I'm not quite sure) in order to sustain the entire nation. It may not be downtown Tokyo but it's beautiful in its own way. I'm in a valley that's surrounded by small hills, life here moves at a slower pace, the countryside is very quiet, everything I need is within walking distance (my work is only 8 minutes away) and all the locals are super friendly. The sun rises at 4:00am and sets early at 7:00pm so I've kind of adapted to it and have been waking up at 6:30am and going to bed around 9-10:00pm.

Each small town around here has it's own unique features; they are all known for something that is associated with only that town. My town has one of the best onsen in the area and holds a large tulip festival each year. We also have other attractions and festivals in my town that occurs nowhere else in Japan.
I would say that the tourists who only stick to the larger cities are definitely missing out on a lot. It's definitely no surprise that the Japanese are their own biggest tourists.