hello.
reply to thread should be reply to all comments of thread, not only to last comment in thread, as it is commonly used now, for that, “reply” button of the comment, from which new thread is started, should be placed below all comments to that new-thread-starting comment. reply button of that new-thread-starting comment can be saved also in its old position, it can be used for starting one more thread from that comment.
i have written about that in russian: ветвление комментариев в жж.