I had also noticed myself, that when you reply to a reply on a thread, it goes under the main body of the message rather than the person you're responding to.
I wonder how it would be if you could have a response to a response go under the response instead of the original post. Sometimes threads go sideways and start other conversations, so it would be nice if you could choose where your replies go. That way if a thread starts a separate conversation, people wouldn't have to see it unless they open the sub-thread. (Like on Facebook where you can open another window when you reply to a comment by a certain individual).
Does this make sense? Haha the language is all convoluted.