Do you think it serves the purpose well, or do you think there's a better way?
Maybe it would be nice (though hardly matching HN's spartan philosophy) to allow the community to assign titles to subthreads, for example: "subthread about housing costs in SF". That would allow me to skip it without having to read multiple comments before realizing I got into the rabbit hole of a topic I'm not interested in.
A flat system could go one of two ways - all comments could be replies to the article itself, which would kill discussion, or any comment could reply to any number of other comments, or even other threads, which is how the flat layout of imageboards work. Although that also usually requires adding direct references to the ids of the comments or boards being replied to.
Hacker News could probably do more to make threads more readable and make navigation easier. One feature I've seen in webmail archives is links to sibling threads along with parent and OP - although that could get cluttered. Reddit also automatically paginates threads which go too deep, so the viewer doesn't see comments beyond a certain nesting level on any specific page.
Discovery tends to break down with long threads, regardless of the layout. I don't think there is a solution that won't require the reader to have to read a bit and possibly encounter content they find uninteresting. I liken forums to parties where you're wandering through a crowded room, listening to conversations other people are having. You can't expect to just immediately be entertained, it takes time to get context. With forums, features like karma are supposed to guarantee that the higher quality content is easiest to find (assuming some objective meaning of "quality" not defined here) but you still have to lurk and read.
In the end, though, that's supposed to be part of the fun.
