The first is stifled by the lack of metadata (tags, categories, subboards, pick your poison) so everything rises or sinks within the same channel.
A broader userbase means groups of people who want to see posts about x and others who think x is destroying the community, and the strife caused by what may be the inevitable fact that some users want variety and others want bubbles.
This leading to the third problem, complex threads which can in practice be composed of more than 40 comments and more comments than upvotes without necessarily being a flamewar. Hacker news appears to be set up to promote upvotes and comments directly to the OP post, and discourage discussion between users. If that's what their ideal model represents then they should just move to a flat commenting system which makes it more obvious, visually.