[xibernetik]

There are different textures to pages from different books, and the design of some books to play with the shape of the media. (Douglas Coupland did it in either Microserfs or Jpod, forget which.) Also there is some difference in how you format the pages - Kindle books you can choose your own font and its size/spacing, while in a print book it has been chosen for you. It's small, not everyone cares about it, but you can notice the typography has changed if you compare books from 30 years ago to books printed in the last five.

You could really make the same argument about using a monitor to read books versus holding a physical book, just with the difference of a Kindle being designed around being held versus propped up on a desk.