Yes, reducing the total amount of replies is a feature. Reducing the amount of good replies (and/or the diversity of replies) is a bug. Making it easy to make a mistake is a major bug. Too many people don't bother to understand a post before they upvote or downvote it -- they go with their initial prejudices. To form a coherent reply requires reading and understanding a post -- assuming, of course, it is a post with substance (which is why I "complain" about substanceless posts).
Look at my most recent post here. It's down to -5 and has exactly one pretty useless comment. I have gotten some really good criticism. I've also had posts where the only comments are endless repetitions of "he is obviously making this assumption" -- regardless of how many times I say, "No, I don't believe that. I am deriving my point from this other direction." (Though, I must also admit that some of my original replies were not that clear, courteous, or cool-headed ;-)
It seems as though you don't like karma systems. But surely they do much more good than bad. Poor karma has precious few consequences around here. Maybe there should be more - like throttling comments.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.