I think this all stems from people not trimming away quoted material. If everyone's going to quote pages of needless text, it makes sense to put your replies at the top; otherwise you'd have to skip past pages of worthless filler to get to the actual message.
When was the last time you saw someone use the backwards quoting order who -did not- quote the entire message? In other words: me too > and in conclusion, I like stuff. That never happens. The people who quote in the wrong order always include the entire message in their reply. The latter causes the former. And, to beat an even more off-topic dead horse, i think people don't trim away quoted material because they don't know how to do it quickly. I've seen many, many pine users pressing the delete-line key (Ctrl-K, i think) over and over and over to delete a quoted reply. Then they get sick of doing this and just leave the whole reply in there. And Windows users don't know about shift-ctrl-end to quickly highlight from the cursor location to the end of the buffer, followed by any key to delete it all. They think you have to highlight it all with the mouse, which is hard, and then click edit->cut. Major pain. So they get sick of doing that and start putting their replies at the top. But the major cause of the bozo-quoting-order is the way that certain mailers don't use any "> " prefix. They just say, "On [date], [person] said:" followed by the message. So if you type your reply before that, you get a nice delimiter. But if you type your reply at the end, you have to make your own delimiter. Which is a pain. So people reply at the top.
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