Responding to your comment about suggested marginalia set, its not intended for every type of text. But in the above mentioned context, the tags I introduce in the document (q, r, t, d) when performed with a grep search on plain-text files I have for notes on these technical books, I can generate quotes, references, terms, and definitions for over ten years of reading in under 5 seconds. That's darn useful.
Adler and van Doren begin their book with the importance of defining terms. You can't understand a book if you don't know the terms the author is using. I would argue that universal to all texts. The Kindle has a great dictionary feature which supports this idea. When it comes to technical books though, many terms are not defined in the standard dictionary.
For paperbacks, I use a Kindle Paperwhite, and that's a great product if you don't mind the MOBI format.
My point is, it's hard to generalize reading requirements. I couldn't possibly write an extension to enable my markup style, because it changes to suit the book I'm reading. That's why electronic will never replace paper for me. Except for my trashy romance novels.