I would already consider it an improvement if we could just comment publicly on papers. I'm surprised Google scholar isn't offering something like this already.
I think this might take off in physics if the ArXiv interfaced with, or copied, PubPeer. Doesn't address most of my concerns, though.
http://www.ncbi.nlm.nih.gov/pubmedcommons/
Wouldn't be helpful for physics and math, though.