[Grue3]

With Gifu-Hashima and other "rural" Shinkansen stations the reason is usually political. For example Gifu Prefecture would not allow the line to pass through the prefecture without a station being built. From Gifu city center it's actually faster to take a train to Nagoya and change to Shinkansen there, especially since every train stops at Nagoya and only a few at Gifu-Hashima.