Hey we have a pro-tour cup here!
I'm in the middle, east of Kyoto near the big lake. There's a fair sized group of kiters here I reckon, and as far as a 'fringe' sport in Japan goes it's pretty popular. More than windsurfing IMHO. We have a few problems with the Rule police - "You can't do that in the public park here it's not on the official list of approved activities" - but the places you can do it are great!
The lake has little beaches but good wind most of the time. And Hamamatsu in Shizuoka has a big scene on the Pacific Ocean and the estuary lake thing ... I'll get pics next time I'm down. As I get more experience I'll be able to post up better places!