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E-ink devices on the order of the Kindle 3 and the Nook probably aren't so good for reading a book that has footnotes, bibliography, and an extensive index even when they are properly formatted - meaning that the links all work as they should. I don't know how much my sense of this coincides with what he's saying, but for me this is because with print I have easy access to the entire book at once, and I am able to examine it (not just read it) in an entirely non-linear fashion. When I have to tackle a tough read like that in print, I may initially skip around in it, using the table of contents and index - or even just thumbing around in it - to get the lay of the land, and that in turn helps with both comprehension and retention.
With almost any ereader I must access the book by starting at the beginning and reading through it page by page, as nonlinear navigation is too difficult, and the page is too small. I think of this as equivalent to trying to read through a mail slot in a door while someone on the other side holds up the book and turns the pages. One good exception to this I've found (and probably mentioned in various comments in these forums) is Barnes and Nobles' PC-based Nookstudy. This gives you a less linear way to access a book, since contents, index, and notes are easily accessible and you can even view two places in the book simultaneously. With the Nookstudy on a decent-sized screen I can come close to the print experience, and when I'm reading a heavy-duty book I work back and forth between the Nook and the Nookstudy, something made easier since B&N made it possible to sync the two. The Nookstudy is actually one reason I chose the Nook in the first place, as I felt Barnes and Noble had a better grasp of the e-reading experience than most. There are some newer reading devices I've seen aimed at the academic market that probably do a pretty good job at making books accessible and improve retention as well, but right now these are pretty expensive, and the products that make them may or may not be successful.
One thing I think the Daily Telegraph article misses is that even though you do have to work harder at retaining information you get through an e-ink reader this has to be balanced against the price and portability they offer. I have recently read several books on current affairs and history, both from the library and through purchase, that I would not have gotten around to without an ereader. I will probably go back to some of these and either reread them, or at least reread portions of them, from time to time, something made easier by the fact that they're right there at my fingertips any time I need them. 9/10 of retention is after all being able to remember where you put the book!
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