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.
The internet is the platform that provides the variety: Hacker News for some topics, and for example RCGroups, SpaceFlightNow, or hundreds of other topical forums for others.
While it is silly to complain about "community X is going downhill", I do miss the old "information bubble" that HN was many years ago. The YC alumnus Reddit has taken over the role of a general link-sharing and discussion on every possible topic platform for every topic - but there is no longer any website (that I know of) focused on the advice, thoughts and discussion of technology startups mostly by founders of technology startups.
Tags for posts might serve the same purpose but allow the community to remain more cohesive.