I really want to see some technology mojo pumped into academia. I've spent a fare amount of time thinking about it, so here's an idea dump for you.

* A markup feature for people to highlight and comment on specific portions of a paper. This would allow students to flesh out missing details and allow researchers to ask more directed questions. The markup could also allow for links to more expanded discussion of concepts, such as on a wiki. People could also go back over time and add markups to the paper to direct people to new developments. The paper would essentially become self-documenting. This encourages more people to read, and may even encourage more interdisciplinary work, by allowing for paper documentation that would ease the burden for a researcher unfamiliar with the paper's jargon.

* How to solve the Chicken and egg problem? Target students, especially graduate students. They are young, more tech savvy, and are more idealistic about research (more willing to be open, less territorial). Give students a tool that will really help them (reading research papers is very hard, time consuming, and intimidating for students).

If a paper isn't available on your service, encourage students to contact the authors to submit a print to the arxiv. Do this whenever someone searches for a paper and it isn't found, and try and make it as easy as possible for the student to contact the author (scrape the corresponding author's email from the original journal?), as well as providing a template email (something that says "Hi, I'm very interested in your paper, and would like to discuss it in detail with other students. There is a great technology that allows for this, but requires that your paper be on arxiv. Would you consider uploading a print of your paper to arxiv? The open discussion should increase the range of interest in your work.")

Encourage professors to encourage students to use the markup. A professor will often assign a paper to a student to read, sometimes as a class project. If the result of that work was a rich collaborative discussion that created a resource for other students and researchers to more easily understand a paper then I believe professors would be excited about the service. In fact, it would make their lives easier because they would have a ready made bag of potential projects for students.

* Integration with a collaborative wiki would be fantastic. I'd like to see a wiki for every subdomain of research. I should be able to go from a paper back to the correct point of discussion in a wiki, and vis a versa. The journal/paper system in academia is a mess, lacking any cohesion. Having a popular open journal will not in itself solve the issue of cohesion.

Populating the wiki could again piggy back on the work of graduate students. Rather than a professor suggesting a student write up a 10 page paper on some topic that will never be seen by anyone but the professor, instead the student could flesh out a section of the collaborative wiki. This is great for the student (the work isn't meaningless) and also great for the professor (there will be many gaps in the wiki, providing for an easy grab bag of projects to assign. Indeed, you could even make it easy for the professor by having a section in every subdomain listing holes in the current wiki).

* I see work to reform academia in the same light that I see work to reform education (such as the Khan academy). Perhaps you can find allies there, as well as potential investors. Ultimately, if academia could be freed of the parasitic journal system the amount of money freed up could easily fund the development and maintenance of a very polished and sophisticated system.

All in all, I strongly believe that if a powerful collaborative tool were available for students/researchers then the chicken and egg problem could be overcome and real changes could be made in the academic community. I'm going into my first academic job this fall (as a post-doc) and would love to have some software I could point other academics and students to. If the software were right I would proselytize it. My email is in my about if you want to chat more.