The most common structure of a document (be it an article, a book or anything else) is a tree structure:
…These types of structures are begging to be assessed by a tree controller like those found on the HTML help files (those that usually appear when you press F1 on any application) or on the Windows Explorer. We should be able to only see the part of the document that interests us at a given moment, and not the other three hundred pages. A large document is a pain to navigate (just think of the tiny scroll bar with very fast steps) and a pain to find information. Documents should be like web-pages except we would have several views possible including the old, tedious print view.
This document format would be suitable for web, desktop, mobile and printing, what else could we want?
Edit: Another idea... This way of editing a document can be implemented on the web. Editing a document on the web with an interface like this would be great for collaborative work! You would edit only part of the document at a time and the system would tell the others that this particular part is being edited but everything else could still be used and changed, as if each document was a small wikipedia. I've been working with partners both close to me and on another countries and, as you probably already know, tossing around emails with word document versions attached is not a productive way of collaborating on documents at all.