I think that Osaka (大阪) is the best 'base' for the trips around Japan. One can get pretty much anywhere and return on the same day. The 'Bay Tower' hotel where I've stayed three times is great and perfectly located - right next to two railway stations (the Bentencho JR Station is the most convenient one), and on the direct line from Kansai International Airport. True, there is nothing much of a significance in the close vicinity of the hotel except a railway museum, plus a small store and McDonalds (which are open 24 hours), but the convenience of its location and the cost outweight any other considerations by far.