What it does show is that professional readers are gadabouts - they scroll back and forth, fork off to check references and bibliographies, hook into google scholar and wikipedia, wish to both annotate and take notes.
So any academic reader system would have to support:
- annotation - storing documents in a revisable format that allows the embedding of location specific links
- split view of footnotes/references - I recently came across an interesting variant of this in which the author published his book online as a pdf but the references were stored on a separate website ...
- internet connectivity
- decent editor and accompanying not organising system - putting notes into aself documenting structure - prehaps something like singleuser sharepoint