"Nested comments sorted by upvotes" is, for free and frank discussion, inherently far worse than non-nested in-line comments. With the latter there's no hive-mind effect, no consensus-seeking, no dopamine/approval-chasing. Also, traditional forums tended to encourage longer-form posts (which you can still see in places like Spacebattles), which naturally contained quite a lot of technical detail and pictures, whereas Reddit (and HN) are optimized for very short comments. In Reddit's case, smarmy one-liners, usually.

But the main problem, to repeat for emphasis, is that the upvote/downvote system (even if it's fair and used virtuously, and it usually isn't,) stifles disagreement and debate.