We're planning to add collapsible subthreads, which will enable some of the things you're asking for.

Things like richer formatting support scare me a little. HN's nearly-plain-text design seems pretty core to the site.

There should be many fewer "unknown or expired link" errors already, and soon you should nearly never see them. If you still get one, say, a month from now when posting a comment, please let us know at hn@ycombinator.com.