The biggest problem for me is this: I have always studied books using the physical pages. The way my brain operates using a book & physical paper as opposed to a screen is simply different. I am very capable and experienced working with computers, which isn't an issue; rather, the point I am getting across is that physical pages which do not have a screen have a different effect on people.
With the way the iPad is right now, one could say "Oh they can reproduce those interactions", but it just wouldn't be the same; some of the things I'll list below might be recreatable (ex. highlighting), while others really can't. The thing is, when you have a good thing, sometimes it was the best thing, and no new technology can take that away. Things would include being able to flip back and forth between two or three different pages with a bookmark very quickly, not having to scroll down a page without seeing the whole thing in front of you, being able to photocopy any content you want at any time, having the capability (if you buy the book) to highlight material, ability to flip to and from various pages physically and very quickly in their own way (it's a different approach using your brain flipping pages than it is using a computer or tablet to flip through pages & indexes).