Whilst the disqus approach certainly had it’s drawbacks (multiple replies to one comment stacked and pulled apart the more public conversations anyway), I can’t help feeling we’ve lost some of the immediacy to the conversations taking place.
Now perhaps it’s really only the work of a few seconds, but those extra beats ruin the entrainment of the experience of following two or more minds dancing with each other.
How difficult would it be to have a column-shaped pop up on the right of the comment box, that stacks bubbles of previous comments in the conversation between the commenter and the repliers comment which you are clicking/expanding/rolling-over?