How many time do you see a new submission that is basically a repost from another one. This is quite high in fact, specially with topic that some user feel really strongly about. It is diluting the potential for meaningful discussion.
But you have as well the issue of submission that don't match PST timezone which means in turn that the submission, although it would match the interest of the HN population and the type of topics that one would expect to find on HN, take a huge dive in the list of upvoted topics, and once again no meaningful discussion comes out of it.
The current upvote system shows very little information. And more than often, user can comments to just thank the author, instead of just upvoting. It might be because there isn't any visual cues of what the current points a comment has gathered or who has upvoted that. One could argue more transparency could lead to a clan issue where some user might want to consciously upvote a sumbission / comment as a group for their own visibility as a group.
There is also the issue of duplication of opinions in the comments, and discussion that take a tangent from the original topic. Both that are mentioned and addressed through the pending comments, but a simple collapsing of child node in the comment tree would have more welcome than this highly debatable feature.