- Reading them sucks except on e-ink screens, for a variety of reasons, including that screens shut off while you're using them, the glow and eye strain, battery life of such devices, distractions, and more.
- E-ink devices aren't great at: footnotes, keeping a finger in an index/end-notes page (generally, bouncing between multiple reference pages), and so on. They're fine for contemporary fiction and that's about it. [edit] big example: only one page visible at a time. Two-page layouts can be practically necessary for many (mostly non-fiction) books, but even in fiction having more text available to look back at can be really nice.
- Physical books are a memory aid—I often forget the title and author of e-books I'm reading because I don't see the cover or spine or top-of-page notations, and spatial memory kicks in for certain things as far as depth-into-book and location-on-page. An edge case, but sometimes I have to locate a book by size and spine color.
- Personal effort that's probably not common, but most of my books are arranged chronologically by (often approximate) date of author's first major work, making the shelves themselves a learning tool. I've not seen a digital equivalent to a book shelf that does anything like this effectively, and certainly it wouldn't be there all the time in the room for passive absorption when you're not actively engaged in browsing.
- They're also often cheaper than ebooks if you're not just pirating those. Used books are pretty cheap, and you can recover (usually only a little, admittedly) money from them if you get rid of them. Used fiction paperbacks can be so cheap they're effectively disposable.
In ebooks favor, they're incredibly space and weight saving and they're searchable, and those are definitely big points in their favor. But if I'm going to go to the trouble of reading anything other than contemporary fiction or very skimmable/low-value non fiction (think: popular business books) I'm going to want a real book, so I can take advantage of the features of real books, not for smell or feel or whatever.
[another edit] oh and you can leave several currently-reading books around the house without having to buy several $100-200 devices (wait why isn't my book on this one anymore? Oh one of the kids picked it up and changed it to Wind in the Willows, hold on, gotta go to the menu...) or go grab your e-reader from the other room or whatever. Ebooks may win for overall convenience, but they don't take it without giving up a couple goals to physical books.