The Discourse forum software uses an interesting hybrid where each
thread's replies are a flat list, but posts that reply to an earlier
post than the previous one contain a hyperlink to their parent.
Good email software lets one change the subject in a reply, but retain the in-reply-to header, whose value is a message ID. But, as you say, not much innovation is happening in email clients. And Outlook, if I recall, at least used to get threading completely wrong, even given the in-reply-to information.