Originally Posted by
abmj-jr
One more that I like:
www.ikyu.com
If you're looking for the best "bang for the buck" I recommend that you search in minor towns and rural areas rather than the largest cities and most celebrated onsen resorts. Since you're starting in Okinawa, you might consider flying to Kyushu and exploring that island for a while before progressing toward Osaka, Kyoto, and Tokyo. Kyushu would be a good place to enjoy an onsen ryokan IMHO.
If you want to visit Kyoto at some point during those 12 days, you would be advised to book your accommodation there first and plan your other stops once you know your dates for Kyoto.