Inbound Tourism is becoming much more of a mainstream term in Japan these days, and there is a growing interest in discovering and exploring the Japan that is a little further away than the usual courses offered. Most people come through Japan via Narita Airport in Tokyo, spend a few days there and then head west towards Kyoto and maybe Osaka.
But there is more. Much more. What we propose for those who hope to get away from the crowds and the places that everyone is going is to make a starting point from Kyoto or Osaka and then go west from there. Of course, if this is your first trip to Japan, it is good idea to check out the big sites and temples and experiences of Kyoto. A couple of days there should suffice. But then, when you want to DO more rather than just SEE what others are seeing, you should head on down to Shikoku.
Natural places to visit from Osaka and Kyoto are Tokushima, and then coming west through Kagawa, and then to Matsuyama before heading up towards Hiroshima. That loop would be a tremendous trip and very worthwhile for people hoping to discover this area.
I found this nice video of a company that specializes in small group tours. While I cannot vouch for them, as I do not know them well enough, companies like this are keen to help you have a very special and private experience as you explore this great culture, try its food, and learn about a land that is far away from your own.