I find them really hard to follow. Threaded commenting isn't so fun when you can't collapse a single comment's thread. Instead, if I want to know who is being replied to, I need to place my finger on the screen and scroll up, seeing on who's comment it lands. That tells me which comment the current one is replying to.
4chan (well, imagboards in general) have a nice system where you can reply to multiple people at once by referring to the post id. Top-level comments are usually represented by referring to no comment, or by referring to the OP's post id. I find this much, much easier to follow.
Both Facebook and YouTube comments support threaded replies, but people tend not to use them. Either just a UI issue (the reply button is not highlighted) or a deeper structural issue (people know that top-level comments won't be reordered, so they think the conversation will still be readable) or a prestige issue (both YouTube and Facebook collapse all replies to top-level comments by default, making it MUCH less likely that your comment will be read as a reply.
Threaded replies are a somewhat recent addition in both cases. In the case of Facebook, it's only been available for a couple months, and with YouTube, maybe a year or two. People are probably just used to the old way.
As do YouTube's IIRC. See Jeff Atwood of StackExchange on his thoughts re: threading.
My thought is that HTML needs a comments primitive with date, author, subject, and references, with the resulting view (threaded, flat, collapsed, etc.) a client detail.
I've spent a fair bit of time reflecting on it. I don't think it would work if resurrected:
1. Usenet was small. Somewhere between 50k and 500k users, based on my own and Gene Spafford's guestimates. More solid numbers appreciated (~1988-1992 or so).
2. It was selective. You had to be a student at a research university, or work for a tech company, or have government access, or be able to gain access to systems provided by same. Which meant you were at the tail end of a highly selective filter.
3. It crumbled under the face of multiple attacks: spam, abuse, trolls, etc. There were some defenses, but ultimately insufficient.
4. It was a pain to administrer, and for little or no gain. Which meant that few providers would, those who did charged, and they recouped minimum benefit for the effort. Ultimately it fell prey to the problem of shrinking usage and ready substitutes largely via mailing lists (relatively comparable) and Web-based forums.
5. Limited rich-format support, limited permanent content support, limited collaborative effort support. A Usenet-type functionality with _some_ support for post formatting, for images, video, and audio (but not to the point of being readily abusable), and for permanent content (FAQs, Wikis, etc.) to be usefully co-related to the primary discussion, would be useful.
I don't know that we'll ever have "one" conversation platform again. And no, Facebook doesn't count.