Why choose the Shinkansen rather than a domestic flight?

It might seem interesting to travel between two Japanese big cities by plane rather than by train.
As a matter of fact, a trip from Osaka to Tokyo will be:

• ~2h55 with the Shinkansen ;
• ~1h25 by plane (half the time!).

However, numbers alone are not enough to show which is the most time saving transportation method.

Indeed, most of Shinkansen JR stations are located in the heart of the cities, or very close to the main touristic areas. It can take only a couple of minutes walking to get to your accommodation from the station! 
On the contrary, reaching a city from the airport can be time-consuming, from several dozen minutes, to 1h30 as it is the case from Narita airport to Tokyo. Moreover, reaching the airport at least 1 to 2 hours before boarding is necessary.
Door to door, it is (way) longer to travel by domestic flight in Japan than by Shinkansen.

Moreover, Shinkansen trains (even in ordinary class) offer a lot more space and comfort than airplane economy class (often the only class available on domestic flights).

For all these reasons, the JR Pass is the recommended choice to travel throughout-Japan.