Seriously, whoever is in charge of Youtube's comment system is a complete idiot of galactic proportions.

Every time they update the comment system, it doesn't get better, it just gets stranger. As if the person in charge of it has no clue how people interact online.

The comment system, as I see it, should be very simple:

1) Comments are shown as a tree (with limited depth possibly)

2) Upvote/downvote/reply/flag-as-spam on every comment.

3) Sort by top / new (would be nice within today, week, month, year, ever).

4) Limit comment length to something sensible like 10K characters, if you want your users to have meaningful discussions.

That's it.