My first must-fix annoyance is that Mail’s Reply feature is hard-wired to encourage top-posting, an uncouth and illiterate practice.
Here’s an AppleScript I ginned up to fix this by removing the blank line at the top of each response and moving the insertion point to the bottom of the message. (It uses GUI Scripting, and so requires Access for Assistive Devices to be turned on.)
It looks like it will require some adjustment for signatures, though.
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