There are various reasons why I choose to take the plane over taking the Shinkansen (high speed rail) and the main reason is cost. Shinkansen tickets are expensive (15,000 yen one way, $180~) and are never discounted while if you book airplane tickets more than 1 month in advance, the price can be as low as 11,000 yen, $133~.
The Shinkansen takes 4 hours from train station to train station and the flight takes 1.5 hours so if you add in access time, the time required is around the same.
The side benefit of taking the flight is that you get to see spectacular bird's eye views of Japan ^^
In this post, I complied the pictures I took from various flights that I had taken.
