Really depends on the type of traveler you are. On my first trip in 2011 I definitely grabbed myself a JR Rail Pass and traveled all way to Kyushu, visiting all the major cities along the way for 2 days at a time.
But these days domestic flights are dirt cheap, so if you're OK with traveling at awkward times like 6 in the morning, you could easily make your way to Okinawa for like 3000 yen (or Hong Kong, for that matter. Some of those deals are incredible).
I do agree with dstopia that the GB crew aren't exactly the best people to go to for Japan advice. They never made it out of Tokyo, are just there for business, and it's been a full DECADE since they last went.
Friend of the show Dave Lang, on the other hand, aside from clearly being a guy with more money to spend than the average person, has done some pretty informative Japan travel episodes on his Team GFB Radio podcast. But I'm too lazy to look those up, sorry.
Anyway, I'm a big fan of going where the wind takes you, but you do need quite a bit of free time to make that work. If you wanna get the most out of your trip, just look up what the major cities are (if you don't know already), and do a lot of reading on Wikitravel. Then figure out whether the JR Rail Pass or domestic flight approach is best for you.
Also, be sure to grab yourself a 4G data sim at the airport.
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