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You can't have a reply mechanism in place, complete with a link to the page of replies, without the threading mechanism being inherent. The threading is already in OSNews v3, and people are already making use of it. Now that @so-and-so etc. is out of fashion, it's become near-impossible to sort through what's being responded to without having some sort of threading view. While you personally may not use it, a lot of people would be a lot happier if they could follow conversations with some bit of coherency.
I don't see why this is so important, after all comments should be about adding useful information to a news item and not so much about discussing totally unrelated topics.
Why would they be unrelated? That seems like a much more Slashdot-esque behavior to me than what I've come to expect from OSNews readers.
Besides, threading allows you to simply skip over unrelated conversations...
One thing I might advocate is a limit to thread depth; e.g. three replies deep is the max. This would ensure that threads never got too convoluted and out of hand in terms of followability.