Going to the Kiso Valley
If you prefer to travel by train, especially if you have the JR Pass, the fastest option is to take the Shinkansen from Kyoto to Nagoya, where you have to transfer to the Shinano line to Nakatsugawa Station. From there, you have to take a bus to Magome, which is one of the most interesting post towns in the Kiso Valley. From there, you can hike to Tsumago, another restored town which is interesting to visit. Otherwise, there are buses and taxis that can take you there too. From Tsumago, you can take a bus to Nagiso, another stop on the Shinano line, and from there return to Nakatsugawa and further to Nagoya, or visit other towns in the Kiso valley, like Kiso-Fukushima or Narai, or even go as far Shiojiri or Matsumoto, an interesting castle town, from where there are direct trains to Tokyo.
