I too am planning a trip to Nippon in the near future, Kyoto is the number 1 place I want to go to there mainly due to the untainted natural beauty of the place. Also, seeing as how my ideal life would involve living in a simple Minka in a misty forest, from what I've seen of Kyoto it is very reminiscent of that ideal.
I'll be checking back on this thread regularly (thanks everyone for your input, especially lordjeebus!)