What I'm really tired of is that off-topic, nitpicking discussion threads are often on top. I have to wade through a lot of comments to find the good ones. And I say that as someone who has myself fallen to the "someone is wrong on the internet" syndrome.
What I would like would be to have a tagging system on comment threads, so that I could filter out comment threads with rough edges if I didn't like them, or threads with endless back and forth nitpicking, or threads that have been covered endlessly before. Something like the old slashdot "Informative" or "Funny" system. Then the ones that wanted could troll and flame away to their hearts content, without disrupting the general discussion of a topic. The "no censorship" crows could turn off filtering alltogether and get HN exactly as it is today.