I disagree completely. When you have threaded comments, what happens is that people post their (often reactionary) opinions in response to OP, and then other people respond in kind to those opinions. On occasion you get a witty quip or a good story, but there's just no meaningful flow of conversation. It's soapbox vs. soapbox. On the other hand, non-threaded discussions, while more difficult to follow, read like actual, real-life conversations. You have a chance of having a pleasant discussion (or even changing someone's mind!) on those sites.

I post on HN or Reddit when I feel like adding a point of data to a debate. I post on MeFi when I want to talk to my peers.

(Admittedly, even sites like MeFi can't compare to talking with people in real life. There's something to be said for taking control of someone's locus of attention while you're talking, which you simply can't do when you have to talk in discrete, comment-sized chunks.)