The advantage of the shinkansen in time is because of the airports locations. Airports, even in crowded, land scarce Japan, have to be located away from the city centers. So, for example, if you want to get from central Toyko to central Osaka or Kobe or Hiroshima, the shinkansen is always more convenient than the flying, and can save time, since the frequency of the trains means no long waits.
If you don't live near a shink line, then you lose that advantage. From Fukui to Tokyo as the jet flies is faster than taking the JR line to Maibara and picking up an East JR shink. Still given all the hassles of getting from Haneda or Narita to downtown Tokyo, it's a close call whether or not to fly or ride the train.
I like to ride the train because the elevator ride in an airbus that is the trip from Komatsu, Ishikawa (on the Japan Sea side of Honshu), over the alps, and down into Tokyo, makes me motion sick.
The French and the Germans make much of their super trains, but what they have pales in comparison to the engineering that went into the Shinkansen lines. The topography of Japan, even to connect the centers on the Pacific coast side, is more like Switzerland, but with earthquakes and typhoons. There have been no calamitous incidents with the bullet trains, yet, though they have come close due to the tunnels falling in from all the pressure of coming and going trains (and there are soooo many tunnels in Japan).
Charles Jannuzi