I think the flat list of comments is strictly worse than a tree for representing a conversation.

Although in other ways I do agree with your sentiment. The discussions happening there were usually of higher quality and nuance than you see online now. There are many factors to that though, including some that have nothing to do with vBulletin itself.

The problem with a tree is if the discussion gets long eventually several branches reach a point where someone being discussed in one is just a variation of what is being discusses in a different once and you need to bring the two back.