1. Can't re-sell, 2. tend to be significantly more expensive to begin with (no used market), 3. annotations, footnotes and such tend to be much worse, 4. often have severe formatting/editing issues (see: all the 1-star reviews for many books on Amazon, which are often full of "book's fine, but don't get the kindle version, it's terrible"), 5. lending can be tricky 6. two-pages-at-a-time and page-flipping is a really stellar interface that e-readers don't even come close to beating, 7. relatedly, use of spatial memory help with real books in a way they don't in ebooks, 8. on that line of though, shelved books aren't just for showing off: they can aid memory, and their arrangement can even help with finding related content and with learning (my literature is arranged chronologically for those reasons—I learn and reinforce some information just by existing in the same room as my books, basically), 9. can only have one book active per device. Switching is a PITA.
Ebooks' main selling points AFAIK are 1. space (admittedly a huge advantage!), and 2. full text search (OK, but not that great—there's such a thing as an index in most books for which this is seriously important, which will usually be better than full-text search). They're worse in just about every other way (though, again, the space thing is really nice)