No, Mail, I have NOT read that letter, despite what you say.

http://www.apple.com/feedback/macosx.html

Here's a direct link for reporting Mail problems and feature requests: Apple - Mail - Feedback

OT

And while we're at it, can we please put in a contextual menu item for marking letters unread in the message pane? Going to the menu every time is drudgery.

Select the email and/or emails, then press: Command-Shift-U

and right now the contextual menu only works in the title pane, which means I can only mark an entire thread unread.

No, it doesn't. If you've selected the title of a thread on the left, then you need to select the individual mails on the right. However, a shortcut key command will always be quicker than multiple mouse clicking, that's why it's called a shortcut. And, if you really want to improve your efficiency, dump the mouse and get a Trackpad.

Jay Lender wrote:

Feel free to fix this completely non-intuitive behavior on iOS, where it originated, as well!

Uncheck it.