Someone touched on high speed trains earlier in the thread. That might be an even better alternative. In Japan, it takes about 1 hour to fly from Tokyo to Osaka. If you're coming from somewhere near the centre of Tokyo, look for about a 1 hour trip to the airport. A couple of hours before flight time. At the other end, about another hour to get from the airport in Osaka to wherever you want to end up. (I'm using average times as these are really big cities). So, the round trip from Tokyo to Osaka is about 5 hours in total.
The bullet train is around 2 hours and 45 minutes, from Tokyo Station to Shin-Osaka station. You could estimate another half hour or so at either end to get to where you want to go, and you're looking at over an hour quicker to go by train vs. air.
And the ride on the bullet train is far more comfortable and enjoyable. And you can eat, drink, and be merry along the way!
Imagine if we could ever make a high-speed train service throughout Canada...the possiblities are tantalizing. Can't be done? Country too big/too wide? Uh, if you overlay Japan north to south on top of the East Coast of North America, it would stretch from Montreal to South Carolina. Sure, they have more people than we do, but not nearly as much tourism (potential traffic loads). On the other hand, they have quite a few more earthquakes than we do, and that is one of the very few things that will throw a bullet train off their consistently on-time schedules.