Traditional linear forums are still the best format for in-depth discussion, IMO. Threads actually stick around for more than a day or two. Just compare gamedev.net to /r/gamedev.
I really feel like we lost something though. Newsreaders provided a much better way to engage in the kinds of conversations that people have on place like HN or even Reddit. To this day I don't know of any web forums that offer the conveniences of newsreaders like tin or slrn. I miss killfiles (and plonking!) and really, really, really well-maintained FAQs on just about anything.
I'm not sure how much of my Usenet nostalgia is just remembering the good stuff. It may not have been as great as I remember, but it sure seemed like it at the time. I learned so much from it, from so many people in so many different newsgroups. Maybe that's what places like HN are to larval hackers today.
maybe the best way is to simply ditch the whole karma/popularity system all together. you can up a comments contribution to an article, but it ends there.
The person who got downvoted isnt stuck with a scarlet letter and put on probation to repair their 'karma' simply because they had a different way of looking at things.