As somebody in the academia, I would see comments as potentially very dangerous. A comment system could be very easily abused by established researchers in some areas to prevent others from entering their niche sub-field. Do not get me wrong: the majority of scientists I know have very good professional integrity. However, I have also witnessed cases where established professors tried in all possible ways to prevent people from competing with them by discrediting or delaying the publication of very solid science. The arXiv as it is now is a great equalizer, because papers are presented without any string attached and this gives a chance to everyone (or at least to experts) to judge the quality of the various works without pre-conceptions.<p>As a fictitious example of what could go wrong. I am a theoretical astrophysicist. I am not established (I am not a tenured professor). Suppose that I come up with a good model to explain some astronomical observations. What I would want to do is to write a paper directed to my astronomers colleagues explaining how my model works and why it is better than competing models. I want to convince them to work with me to analyze their data. As it is now, I would post it on the arXiv, the astronomers would probably find it, read it and evaluate it. However, if the arXiv had comments, a single negative review by a more established theoretical astrophysicist would be enough to discourage any astronomer from even reading my paper. Remember that in the astro-ph section of the arXiv there are of the order of 100 new papers per day and we can realistically read only 1 or 2 papers per day on average. In this situation, the chances of my work being completely ignored because of that one comment would be very significant.<p>I think that the current channels for commenting on scientific work, private email and&#x2F;or  rebuttal papers, are perfectly adequate.