I love being able to take around hundreds of books on my Kindle Paperwhite and it is the best iteration of the product yet (have owned two previous generations). There are many advantages to e-readers – sync across devices, minimizing clutter, etc.
One thing I still find problematic in reading large non-fiction / technical books with an e-reader is losing context or a sense of where you are. Flipping page after page, arbitrary “location” numbers, percentage completion and/or page numbers don’t really do the trick for giving a visceral sense of status. I know X-Ray is supposed to be a solution to this end, and you can quickly look at the table of contents to see relative position.
But with a physical book you can get immediate visual / physical feedback on where you are, how big a chapter is, how much is left to go. See the higher level structure / organization across multiple pages or within a chapter. You can skim or skip to sections at varying rates by the number of pages you physically move. Jump back and forth between specific sections very easily. All methods to zoom out to a higher level for strategy and then back into the weeds for details.
Right now I’m not sure there is a good solution yet for this with ebooks / e-readers, and hopefully we’ll see better use of technology for this end in subsequent iterations. One of those things that underscores the need to accommodate varying levels of information processing / architecture in the interaction design / user interface of solutions.