Travel around Japan in 6 weeks

If you're starting in Hokkaido, take about a week to see the sights there.  Sapporo, Otaru, Asahikawa (Asahiyama Zoo) , Hakodate and if you like nature see the Shiretoko area which is a World Heritage site.  

The next week move down by train /Shinkansen to see Hirosaki, Morioka, Sendai/Higashimatsuyama, Aizu (Fukushima), Nasu /Karuizawa and Nikko.

If it's autumn the foliage should be beautiful. Then passing through Tokyo, take the Shinkansen to Kanazawa. Stop by Gifu and see Shirakawago (another World Heritage) on your way down to Osaka and Kobe and Okayama. That should take  another week.

On your 4th week, continue down by Shinkansen to Kyushu, but stop by Yamaguchi Pref. to see the Kintaikyo Bridge. You'll need a full week to see Kyushu as there are so many sights to see and Onsen to visit.

On your last 4 or 5 days, visit Okinawa and spend some time relaxing. It'll be chilly but not so much that it's impossible to go in the water. If you want to visit more than 1 nearby island like Ishigakijima or Miyakojima leave a little more time to spend in Okinawa.

Hello Akane,

Thank you for your quick reply. I appreciate your help very much.

For the transportation: which is the best way you think we should do? Should we get the air pass then fly to Hokkaido, rent a car drive around Hokkaido? Then fly from Kyushu to Okinawa, then Okinawa-Tokyo. Or we can just get JR pass and travel around the whole trip? Please let us know the best way to make the most of our time, and money.

Thank you Akane