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.
I think that the current channels for commenting on scientific work, private email and/or rebuttal papers, are perfectly adequate.