Comment Posting hierarchy (nested replies)
When someone replies to another user's post, it indents the new reply. Great. If someone replies to THAT post, it does NOT indent the new reply. It positions it as if it's just another post in the original thread. If you're going to be a forum where people post replies to others' posts, then you need to respect the hierarchy of the original and the replied posts. The problem with the way you are doing it now is that very often, someone's reply is posted way down in the hierarchy with no apparent relation to what that person's reply was responding to.
For whatever it's worth, I consider this request a major UX bug--it makes no sense to "nest" replies to specific comments on the same level as the original comment itself. It makes the comment thread into one big mess that's impossible to follow. You should either truly nest replies, or not allow replies to existing comments.