It seems like the rest of your issues could be solved by Mendeley- WDYT?
You guys should get in touch with the peer library guys, send me an email if you'd like an intro. I'd love to see more collaboration in the space.
Internet Archive (archive.org) is also interested in contributing to the space and has been super helpful in aiding our efforts at open journal.
I think the three biggest problems in the space are (1) discovery + accessibility (including open-access), (2) collaboration (sharing, commenting, contributing), and (3) quality assurance (maintainability, scm-backed, repeatable research).
There are many solutions to target discovery and accessibility but I'm (as an academic) personally dissatisfied with the level sharing/collaboration/openness, the lack of community, and the lack of standards in academic research. I think the world needs for academia and research what github did for social programming.
I've loved the GitHub for science analogy ever since it first surfaced a couple years ago- I couldn't agree more.