15 Day trip to Japan

I'm flying in from the US to Haneda Airport , and then 3hrs later taking a 1 way flight to Hokkaido, because well, it's only $49 and 1 1/2hrs, instead of the Shinkansen's 8 1/2hr. I really wanted to see the small towns of Japan and the non-popularized but often missed Japan, along with some nice onsen's and ryokans's. I will be taking the train back to Kyoto and then to Aichi, Toyoda City (I work for Toyota, so I'm a bit of a nerd for it and wanna make it a point to see while I'm there). Question is, do I want to go to Hiroshima for 2 nights on my way south? I've been looking at many of the posts and it just seems there's TOO much to see in a single 2 week trip. I am planning to go back to Japan in October. Any suggestions?