(Edited) After using the nested comments for a couple of months, we should review the current solution. Personally, I am not happy with the differentiation between comments and comment replies. I find it confusing and the UI with different behavior for comments and replies does not help either. In the post at Okuna a couple of different opinions and proposals came up and I think it is worthwhile to gather them here.
(Original proposal) After using the nested comments for a couple of months, I suggest to go back to the flat structure. In my opinion, the nested structure adds more confusion than that it adds a way for a structured discussion. On top of that, I am always annoyed by the different editors for comments and for comment replies. I almost always end up searching the right button to submit the comment/reply.