Best time to visit different regions?

Hey I am hoping to go on a gap year around Japan next year and i was wondering when is the best time to visit each region/prefecture? What i mean by this is like most beutiful time, weather, least ammount of tourists, which are the best festivals to catch etc. I know quite a lot but not sure how to balance out to be able to see whole country over the year, because most people recommend around spring and autumn for most places. I will probably be going may/june to following time the next year.

Basics are explained here:
http://www.japan-guide.com/e/e2273.html

My personal recommendations are:

Hokkaido:
- first half of July before the school holidays start and for relatively pleasant weather
- February for the most snow

Okinawa:
- late June for the best weather of the year and relatively few crowds

Countryside of Honshu, Shikoku and Kyushu:
- May (after the Golden Week) for pleasant weather, beautiful vegetation and few crowds
- October/November for autun leaves; but popular autumn leaf spots are crowded

Cities of Honshu, Shikoku and Kyushu:
- March through May and October to mid December for pleasant temperatures

Remember that the best times to visit each region weather-wise and event-wise will obviously coincide with the arrival of the most tourists (mostly Japanese tourists). You can't have it both ways!