Well, I like your point. The only problem I see with linear conversations is when the comments are too many to follow responses easily, things get really messy

Well, I like your point. The only problem I see with linear conversations is when the comments are too many to follow responses easily, things get really messy at that point and the very best one can do is jump around following links and trying to understand the dialog. And, you're right, if you don't join a popular thread in a threaded comment system, you will probably be ignored. But you won't if you're one of the first to post in that page, thus somehow making the oldest more relevant, and if you get lots of replies your comment will be seen by more people, which makes sense to me since it would be a hot topic. There is no perfect commenting system, I guess, but the big flaw in linear conversations is that replies are not emphasized and the relations between comments is easily lost. It would be useful when time is relevant. I would prefer a threaded system, sorted by rating as well, kind of what Reddit or HN has: the hottest, top-rated, most recent comments on the top; the oldest, lowest-rated, not-replied-to ones more likely to be ignored.