I think it's bullshit to say that "the brain prefers something".
Most people prefer what they have learned, and what they know best. For most people living today, that is (still) paper books.
Imagine a child that was born today would be given only e-readers to read from starting at age 4, then would be using e-readers in school, and in college, and then introducing him or her to paper books in 2060 (at the age of 47). "Look at how we read stories before 2007!"
I think a paper book would just be an amusing curiosity to someone like that, in the same way a black-and-white movie is a curiosity nowadays. Nobody watches them, except when in a nostalgic mood.
I know people who have never watched Shindler's List, on the sole ground that it wasn't in color. (Yes, I know the two split-second occurences of red in that movie.)