Actually, there might be an easy to use solution! It is called "Self journal of science" and is available here: http://www.sjscience.org/artic...
Think about "Github, but for scientfic papers!"
It features the possibility for any scientist to publish a paper (in Latex because this is what scientists use). The document can be viewed online and each paragraph can be discussed online, using a revision system where pears can review your article (think about a start system on steroids, for scientists).
The project was started by Michael Bon, a researcher who was fed up with the way scientific papers work today.
Disclaimer: I know the developers who work on this project. It is still in development but is already usable. They definitively need some help to spread the word, and more than anything, I know they need papers published on the website. If you happen to know scientists who might be interested, please let them know the "Self Journal of Science" exists! These guys are really trying to make things change and they need your help!