Any way to copy message body from Apple Mail keeping quoted line prefix (">")?
On my Mac with Mail 10.3, I can select a message in a viewer window, go to the menu bar and choose View > Message > Raw Source.  In the resulting window I can scroll to find the part of the message I want, and select the text I want to copy.  I just tested this on two messages from my Sent mailbox, one with Rich Text, one without.

Blank quoted lines seem to get an '=20' escape, so you'd want to do a search and replace after pasting.  It might not be too hard to make an AppleScript or Automator thing to help with this.  

With an older version of Mail you might find the Raw Source command in a different menu, I seem to remember.