No community I've ever seen, apart from MetaFilter, has kept the noise level low enough that participating in the community is enjoyable. Hacker News was great a few years back, but it's painful to watch now. Same for every other site I've known: As the community grows, discussions degrade, and people get hostile.
People don't have a lot of insight. So when sites open up to comments, the typical comment — which may be perfectly average for humanity — is trash. People have agendas and biases. Most people don't see it, or don't care, so they don't correct for them.
Commenting systems and algorithms can hold back the tide for a while. They can force out people with a net negative impact on the community. But in the end, attempting to sustain good discussion is a losing battle. It's so easy for good discussions to turn bad, for intelligent arguments to become baseless, for disagreements to become personal attacks. Humanity as a whole isn't capable of rational, reasoned discussion at scale.
On my blog, someone said they were considering assigning some heavily-moderated "contributor" slots to each post, where each would sort of be treated as an addendum to the post itself. That definitely strikes me as an interesting way to focus discussion to small groups, but also very difficult to handle in any kind of automated way. There's also the concept of focusing discussions into communities with similar topics, but I don't think you'd get the breadth of commentary that you would with other systems through that.
You're right though; the average comment is trash. The question I want to ask people is how they can motivate commenters to realize that what they're posting is trash and either just not post it or refine it.
Encourage use of cites; some way of rewarding useful citations might be interesting. (EG, this post is lousy and only gets two upvotes, but the citation is great and gets ten.)
Ban out-right some topics; or have very narrow constraints around how they are discussed. Some topics will instantly explode into heated bitter flamewars with no possibility of sharing useful information and no chance of changing people's opinions. They're toxic. Which is a shame, because they are usually the things where people actually need more and better information, and where a carefully arranged discussion could shed some light. Obvious examples of these topics are Palestine/Israel[1], Abortion, Circumcision, etc. (Yes, I know you posted two examples. I guess you have great users, long may that continue.)
Your idea about collectively owning a site is perhaps useful, but you'll be in for a rough ride if you need to make changes that your users don't like. Because you've made them co-owners now, and they have a say, and they are entitled, and etc.
You do need to find a way to split deterrents for posts that "do not belong here" and posts that "I disagree with". There's some suggestion that, on HN, acceptable posts are being downvoted because they're unpopular.
In general, moderation is often awful. You need someone to kill the spam but after that lots of stuff becomes subjective and thus open to arguments.
I think limiting the number of contributors is interesting, but I wouldn't limit the ability to reach a big audience per se. Precisely the possibility to reach an audience entices high-quality comments. Possibly part of the real challenge is actually to keep the non-commenting audience interested in the comments.
So maybe it's about limiting the number of contributor-slots available in any given situation, and then of course think of a non karma-whoric way of assigning those slots... hmm :) Maybe even make it random, so anybody can get one of those slots, so create a sense of urgency not to blow that chance. Might work in some situations.
Highlighting comments from established contributors is a problem if some of them are dicks, or some of them occasionally make awful comments. You also have a problem with "vested contributors" - 'I broke the rules, but I've been here so long and do so much good that it's okay because you know that really I'm alright' whereas the newbie just gets banned.
