An ebook reader/protocol that would let me write or read comments left by other readers or the author(s). It would also be nice to be able chat with other people currently reading the book, especially for more technical books. Basically, make ebooks a bit more like MOOCs.
This allows you to paste in a link and discuss the website, as well as gather materials for research.
I'd like the ability to join many others who are learning the same thing. I think we need a method of referring to sub-topics so others can join in on the conversation. So many answers and information is stuck in forums with a generic thread title. Information will only grow- how can we better self-categorize the content we create so others can find it?
I believe that the first half of your want is already satisfied by amazon's kindle. When I had a kindle 3, I could turn on a feature to see highlights and comments from other readers.
That would require internet access and a login and cookies and all the annoyances that go with these things. It seems rather unfeasible given the convenience that most ebook systems go for.
I agree, it would have to degrade gracefully back to a regular offline ebook if the online features are unavailable or disabled. Ideally the reader/protocol would have to work with existing book formats and just enhance the reading experience.