The simplest solution to the 'chronological pile-up problem' (nice name BTW) is a Wiki model, where replies are appended by default but the entire content can be edited if necessary. (C2 demonstrates this quite well.) For simple problems, conversations behave exactly the way they used to, but when it starts getting complex someone can go in and rearrange the conversation into a more logical form. This actually maps quite well to email: by default replies are appended to the bottom, but they can also be inserted inline (some mailing list etiquettes even demand this) or indeed the entire conversation can be rewritten. You'd probably want some sort of merge algorithm in case someone replies to an older email.
In fact, my usual approach to dealing with tickets/issues/emails which start to develop this problem is to make my own private copy of the thread and edit it in precisely this manner, though I'm the only one this benefits since it doesn't get sent back upstream.