Many times you want to link from your web page to an external source or related page, but you have multiple such sources or related pages connected to the same word or phrase.
It would be very beneficial if while reading a book you could not just highlight and make notes about a passage in the book, but also link it to another passage in another book.
Have a new protocol for linking between ebooks. Something that is a standard and works on most platforms like iBooks, Kindle, etc. Make it possible to share these links with others.
Many times you get links that are for a particular device (mobile, desktop) because the sender used that device when sending them to you. When you click on these links, however, you might be on a different device and will get unreliable results like blank or poorly formatted pages.
Have the client software you use, detect these discrepancies and automatically correct them, at least for all the main link sources like Amazon, etc.
Help you remember the what and who of a book that is complex or you continue reading after a long break.
Have an option in ebook readers to turn on a layer of hyperlinks. These should be available to link characters and events mentioned to their origin in the book, so you can click on such a link, and it will either take you to the source so you can catch up again, or pop up a window with the original text so you can take a look, close it, and continue reading.