In Kyuushuu, you should look into Udo Jinguu (sea cave shrine), Beppu (onsen), Mt Aso volcano, Nagasaki (history), Yakushima (suntropical rain forest), Minamata (corporate coverup of mercury pollution) and there is a tonne more to see that you will find when you are there.
I highly recommend Shikoku. Konpira-san (stone steps climb to a mountain temple), Iya Valley (go to the east vine bridges, much better than the west one), Matsuyama (castle and onsen. Lots of other neat stuff I haven't been to.
I loved Amanohashidate. Make it a day trip from Kyouto.
You can see lots of my pictures all over Japan here:
Northern Japan will generally be too cold/snowy for many kinds of sightseeing. Toukyou will be fine.
Thankyou both for the great tips :)
I really appreciate it.
Forgot to mention you should get a print-out or go online for a list of the "matsuri" going on for 2013, this should be kicking in pretty soon, especially if you are there through March.
In addition, I like "ekiben" train station bento box, it's different in each region and very pretty to see and experience.
Have fun and contact me directly if you need any help or more suggestions!
Besides the obvious cities to visit like Tokyo, Kyoto, Osaka, Nara and Hiroshima, then there are just so many beautiful smaller towns to go for a visit. Often even the most quiet towns have something to offer. For example, one of my friends live in a town called Fuchuu, which is not too far from Hiroshima (or actually closer to Fukuyama). If you go generations back, that town was famous for its furniture handicrafts, and still today there is a museum with some of the style and furniture that it was famous for. And a local products souvenir shop. But with pretty much no visitors. But its kind of charming and the town is actually quite pictoresque, and still has a few restaurants existing. And a run-down shopping street.
But if you need something with more action in it, then many japanese tourists go to Onomichi. There you can easily spend a good day.
An then there is this rather unknown city of Shimabara which should be on the list as well: http://www.japan-guide.com/e/e4450.html