Okay, to make it clear: I think HN's main issue at large is that the mission statement ('to post things that gratify intellectual curiosity') is too broad. Forums and sites that are established with a broad mission statement means that as it grows, the site loses identity because it results in a sort of race to the bottom.
And to call back to my original examples: The Katie Bouman thread(s) [1] [2] and the Women: Learn To Program [3] threads should give you quite a lot of pause. The fact that such benign incidents resulted in large flamewars is specifically an issue because it indicates a greater rot growing inside HN's culture.
There's obviously more examples (such as anything politically related almost immediately devolving into flamewars or whataboutism) which indicates that the mission statement simply isn't working. And the greater problem of flagging only works if the community as a whole agrees in a positive direction; if suddenly tomorrow HN was filled with people who held highly negative beliefs, then the flagging system fails.
When I look at other forums such as SomethingAwful, Penny Arcade etc I see them as surviving because they have much stronger moderation while maintaining a sustainable community size. And right now I don't see HN outlasting either of those communities. Without some sort of cohesion guiding the community, the end result is that the site will eventually be pulled away from its original purpose.
To sum up what I think would be necessary:
1. Long time contributors would need to be emphasized more. Especially the high quality contributors, because they serve as a way of keeping a community united.
2. The mission statement of HN needs to be less vague and more to the point. Keep a focus solely on things that happen with the tech community and issuing harsher but smaller punishments to people that cause issues. You issued a warning to me a while ago because I was being an ass, and on other sites a warning like that would've resulted in a harsher punishment like a temporary probation.
3. Politics is inescapable as was found out during the 'political detox' week. But other forums can help moderate and control political debates and inflammation by keeping them solely inline with the site's mission statement (ie: a gaming site focuses on politics as it relates to games).
That said, implementing a lot of this might be almost impossible at this point because people would decry censorship almost immediately, resulting in a large reactionary wave. Which unfortunately I think also says a lot about the overall lassiez-faire moderation style HN employs for everything but the most egregious and repeat of offenses.
[1] https://news.ycombinator.com/item?id=19632086
[2] https://news.ycombinator.com/item?id=19653120
[3] https://news.ycombinator.com/item?id=19464269