This. Three levels of comments is just too complex. I'm still not convinced that every pro/con needs its own comments tree.
One possible solution is to reduce the number of levels, but make linking to various items from comments possible. This way, if I'm clicking "Add Comment" while viewing a viewpoint, I'm not forced to visit separate pages, but can optionally choose a pro/con I want to discuss (the choice of adding a comment to a viewpoint rather than pro/con can be explicit, not default, to enforce choosing a pro/con instead of just mentioning it in the comment's text). I don't want to see "Add comment to X thread" links all over the place. It's too complex.
Most often, I want to view all comments for a viewpoint. If I want to view comments for a specific pro/con, it can be presented as a filter instead (show all / show for pro X / show for con Y / show for pros / show for cons). "Comments" links on pros/cons can scroll to comments at the bottom and switch the filter instead.
The same with a question page. I don't see pros/cons from there, so I likely want to discuss viewpoints. When adding a comment, I can choose what to link it to: to question / to viewpoint X / to viewpoint Y. I shouldn't be able to link to pros/cons from here, I shouldn't see links for adding comments to top pros/cons — this functionality should be exclusive to viewpoint page where all pros/cons are listed.
(Well, the object model remains the same I guess, but from user's point of view, it's one level of comments less. And no extra pages, just comments linked to items.)