I think the whole nesting of comments needs to change too. Don't get me wrong, I don't have the solution or what it should be changed to, but I just know from experience that replying to someone else's reply which was a reply to some other comment, makes the entire structure/conversation incomprehensible.

Something else that is a pain with nesting comments is that the area of the comments becomes narrower and narrower. Once you get 5 levels deep the comments are not nice to read.
One way to solve that could be to have comments "bleed" into the sidebar area (in the case of WP Tavern that is).

In that aspect LinkedIn Discussion Groups do it easier/better by simply placing each comment under the other, in other words no nesting.