This is something that might be far in the future, but I hope that if I suggest it there is a possibility that it will come true. I find myself searching for articles found in the bibliography of the article that I just finished reading. My suggestion would be for Endnote to recognize bibliography/reference sections in the PDF articles currently in my library and then search for the ones that I click on, so I would be able to download their PDFs (or jump to them if already in my library) and continue my reading/research. Are there any other researchers that this would be useful for? Also, is it feasible?
Proprietary databases do have a way to access and to export the citations that go with a publication.
For example, Scopus (must have a subscription) allows you to select and eport some or all of the citations listed in a specific paper.
You might also find the some other software approaches of interest.
TR has this one http://wokinfo.com/products_tools/multidisciplinary/webofscience/citmap/ .
I get really scared when people ask increasingly more of a program like Endnote, which then tries to do everything (editing PDFs, inserting-numbering-captioning figures, keeping notes, grouping and managing references in multiple deep layers, read/unread, rating options etc, etc), rather than doing what is was designed to do well.
As in Soundheim’s “Into the Woods” – “Be careful what you wish for.”