I definitely have an axe to grind because it breaks my code, but I really believe it's very bad for discussions. In particular the case of only a single comment and it's children appearing on the first page of comments on threads with large number of comments is the biggest problem. It leads to only one response to the article being heard and has the side effect of greatly encouraging piggy-backing on the "first post", as it were.
edit: when I say 'my code' I mean my code that's forked from wvl's hckrnews.com extension and any other extension that highlights new posts since you last opened the discussion.