Chris

One of the problems as I see it is the mechanism for commenting. Annotations are easy. Just highlight and comment. But the discussion aspect, probably the most important one, is a little difficult at best. Here are the problems I see

Feeds - If I could have custom feeds for topics that interest me, I'd be doing a lot of commenting right there. Right now, it's difficult to keep up.

Community - PLoS One for all its goodness, still feels like a repository of papers as opposed to a place which fosters communication and discussion. That probably explains why there is commentary on the GXP blog. Perhaps one way around it would be to grab discussion about a paper and display it next to the paper itself. That way, it becomes a portal of scientific discussion in itself.