I was introduced to a very unique travel agency called "OKU Japan". "OKU (奥）", literally means "deep" in Japanese.
They are specialized in multiple-day tours in Japan, especially in rural areas and along old pilgrimage routs, such as "kumano kodo".
The origin of this company is by a British resident in Japan over 20 years who loves traveling and has traveled all around Japan. I am very happy to know they are trying to feature rural areas with small inns (small accommodations in Japanese style), and have good contact with locals. I am sure you can experience more homy and warm and cultural atmosphere close to the nature by the tours they produce.
"Oku Japan operates guided, self-guided and custom tours around Japan. Our main office is in Kyoto, and some of our sales staff are based in the UK. In spring 2015, Oku Japan opened a branch office in the village of Chikatsuyu, where we are proud to be part of the local community. "