A simple but useful suggestion about e-reading from Russell Jones:
There's a difference between linked information (where links can become obsolete) and embedded information, which is persistent. I'm sure you've all had the frustrating experience of clicking on a link only to find that the information is no longer available. In contrast, footnotes or endnotes in a book are always available. Ebook publishers can use both, as needed. If the information is critical (and small), embed it; otherwise, link to it.
The UI problem of all the ancillary material getting in the way of a clean reading experience can be solved easily, by simply making the links/extra info invisible until the user reveals them. That can be done through a gesture, a Ctrl+Click or some other unused-in-ebook-reading action. The reveal would be a toggle, so users could turn it off equally easily. That lets publishers include as much ancillary information as they wish without interfering with the reading experience.
Other reflections in the article are useful too, but I especially like this suggestion. Of course, one's dedication to the reading experience will be constantly tested by the presence of the toggle.