Minshuku, the Best Way to Experience Japan
There are many different kinds of ryokan/minshuku in Japan and you can see definitions of them at http://JapaneseGuestHouses.com/ryokan-styles/
Personally I like minshukus best as they small and more personable. The owners run the minshuku and cook the meals. They take great pride preparing meals and making sure you are comfortable.
Eating at your minshuku should not be missed unless you are on a very tight budget. Here you will have some of the best most authentic Japanese food anywhere also there many not be any other options close by.
Most minshuku are located outside of the big cities of Tokyo, Osaka and Kyoto. Shirakawa-go has many gassho-tsukuri farmhouses that are now minshuku and Tsumago/Magome also have some wonderful traditional minshuku. Staying in one of these is like taking a trip back in time to Old Japan.