There is cheap flight tickets from SNA air company.
It's only 10,000yen for one way on any flights operated by this company, like between Tokyo-Nagasaki, Okinawa-Nagasaki.You can get this ticket only if you are as a temporary visitor. However, advance booking of this flight is not available...
But according to this airline company staff, there are always some available seats except for highest season like new year holiday and Obon holiday in summer.
So let's say, if you are holding a JR rail pass, and you fly from Tokyo to Nagasaki and spend several days. Then, when you travel to the north of Japan island, you start your JR rail pass when you leave Nagasaki~! So that you dont have to go back the same way as you came.
If you are afraid that the expire day of JR rail pass is coming during your travelling, you can finish the pass in Nagasaki and spend some time here, then just fly back to Tokyo~! It is only 1 and a half hour flight, not like tiring trip on the train for a whole day.
Please put into your mind~~
maybe that could be one of the options to enjoy your trip in Japan:)
More detail, please visit this airline company~