My daughter is in grad school and she can't use her reader for textbooks. She adores it for regular reading, though.
I don't think that's correct. For example, the Kindle can (according to Amazon):
By using the QWERTY keyboard, you can add annotations to text, just like you might write in the margins of a book. And because it is digital, you can edit, delete, and export your notes. You can highlight and clip key passages and bookmark pages for future use. You'll never need to bookmark your last place in the book, because Kindle remembers for you and always opens to the last page you read.
Apple claims that with iBooks/iPad:
If you read something especially interesting or inspiring, use the Bookmarking feature to highlight the text and make notes — perfect for students.
I just tested the latter on my iPhone, and it does work, although it'll take a little practice to get used to the controls. Probably a lot easier on the larger screen of the iPad.
A decent reader these days will have note taking and highlighting built in. Above that I’d like to see voice notes — select your text and talk to have it saved as an mp3 (or AAC or whatever) and hooked to that bit of text. Get a ToC of your comments, showing chapter, page and a text excerpt, touch to listen. Extra credit if the system automatically runs speech recognition and saves and indexes the text for later searching.