The standard used to be that replies and the original content were mixed. This made it easy to reply to every point made by the previous person, and easy to see what was skipped.
As opposed to what happens here which is that when I go to reply to someone, I first read, form an understanding, and then reply to my understanding. It is extremely rare to find people going through what someone said point by point and agreeing or disagreeing with each bit.
If you've ever experienced that style of discussion, it is clearly superior for complex discussions. If you haven't experienced it, it is very hard to understand how it might possibly work.
(I often reply here by quoting several points in italics and replying separately to each. That is a strictly inferior to what used to happen, though, because they don't have a way to do the same back and keep straight what they said before, what I said in reply, and how they are correcting my reply.)
HN and Reddit require far more scrolling to go through all the comments, and make it difficult to find recently posted comments (though Reddit has this feature if you have reddit gold or are a moderator of a subreddit).
A typical newsreader shows a thread index overview which, even for thousands of posts, doesn't require that much scrolling, and makes it easy to see new posts within the thread.
