> What's wrong with giving other researchers the ability to rate and comment on a paper.
I do not see nothing inherently bad with this (provided very good moderation tools are in place). However...
* > I would argue it works just as well a this journal reputation system *
As a journal reputation system, possibly; although I find that experts have often very different taste compared to say general Hacker News public -- for instance, machine learning has a very high "coolness factor" these days compared to other areas of computer science, but it would be unwise to make a system where a weaker paper on machine learning gets vastly more credit than a better paper on say approximation algorithms.
However, an important part of the journal submission process is the fact that the editors ask the members of the academic community for spending several days on the paper, noting major and minor details and checking the validity of the proof.
Since the reviewers do their work for free, there is no reason why there cannot be an open system that replicates the same process; still, just "adding a comment system to arXiv" will probably not be enough, as people spend rarely that much time on comments (15 minutes tops, not entire days).