I'll have to agree. But it looks like there's a tension between individual satisfaction, and collective quality. I'm not sure this tension has to be.
Reddit implements different solutions, and so far it frustrate that HN doesn't try some of them:
Markdown support. HN only has star-based emphasis and naked links. Many comments would look cleaner if they could take advantage of at least citations and lists.
Inbox. Presently, I have to scroll down my "threads" panel to see if anyone has replied to me. New messages are not even highlighted, so it's easy to miss them. This, I think, is the biggest long-term conversation killer.
Inline replies. Presently, when you reply to an HN comment, you are kicked to a page where you only see the comment you're replying to. Leaving the current page is a hassle, and may discourage some type of comments —probably not the type you'd want to encourage here, though.
No damn "unknown or expired link". It's frustrating to have that one every time I type a long comment. Instead, I'd rather have some ninja-edit detector.
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Maybe you want to limit such back-and-forth threads, possibly because of their average low quality, but Reddit have mechanisms to deal with that:
Hidden stuff is collapsed. Here in HN, hidden stuff is written in very light grey. Still, it takes up screen space… In Reddit, hidden stuff is just reduced to a single line, on which you can click to expand the hidden stuff.
Hide entire threads. When a comment is downvoted below some threshold, the whole thread is hidden by default. One has to click to recover it.
Charge Karma for replying in a junk thread. That's a LessWrong exclusive: when you reply in a thread that's supposed to be hidden because of too much downvotes on a particular comment, your karma instantly goes down by 5 points. Just so people really think before they reply to trolls. (Those who replied before the downvotes occured are not affected.)
Hide long-winded threads. When a Reddit thread gets too long, the later replies get cut regardless of their quality. One has to click to see the end, so they don't get very public. I like this feature: you can do back-and-forth, but the other users don't have to suffer this little private flamewar.
Hide lesser-quality threads in stuffed comment pages. Sometimes, a real popular pages gets over 500 comments. For those, Reddit hides even some comments and thread that didn't get any downvote. The idea is to highlight the higher-quality comments.
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Now there are some features I like in HN that you probably want to keep:
Hiding Karma scores. I'm not sure why, but my average went up the very day this came up. It's probably not neutral. But most importantly, it seems to be a deliberate and tested feature. You probably know more than I do about that.
No downvoting thy replies. It's frustrating in Reddit when your reply is downvoted by just one point: you never know if it's the parent's author being a jerk, or if it comes from someone else, who is presumably more impartial. HN removes that doubt, so I find it easier to stay civilized.
Dead comments. The distinction between massive downvote and death seems to be working here. Not being able to reply to dead comments at all is probably valuable.
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That's about it. Now you have even more work to do. :-) Now I don't expect all the proposed changes would be a good thing. But I think most of them are worth testing.