Yeah but with threaded comments, it's very difficult to follow a discussion as it develops. I have the same complaint about HN. I much prefer the chronological layout with the ability to quote other people.
I actually completely disagree with this. Threads allow for a single point of interest to spawn multiple straight-line conversations, where each thread pertains to a different facet of the original topic. Whereas a single thread conversation (like a forum) only allows for a single thread of conversation, and divergent conversations are all mixed up in the same thread.
With Reddit (but not HN), the ability to collapse threads makes it even easier to only follow the particular conversations you are interested in. Collapse the ones you don't care about (like pun threads, etc.), and read the important stuff. With a single thread, you have to scan every single comment, including the junk and the stuff you don't care about. Not to mention the whole "Page 1 [2] 3 ... 389" deal that single threaded conversations get into.
You mention chronological order being important, and most threaded sites (but not HN) have the ability to sort threads by chronological order, which gives the same single threaded "top level" of comments.
I agree with you that HN can be a chore to read, though. I think it would be massively improved were it to have a built in thread collapsing mechanism. It definitely has the least feature of threaded conversations that I've seen.