It is impossible to go away from a post by Pierre Igot at Betalogue without learning something new. Two recent post are no exception.
He details several shortcomings 
in the way that Mail presents the user interface for threaded messages and in the method it uses to auto-select a first message to display when any given thread is expanded.
A second post expands on the problems , especially how keyboard shortcuts operate in normal and threaded views.
Several of the issues arise because of the way in which Pierre likes to use Mail:
I use Mail with the so-called “message area†pane closed. In other words, my main mail viewer window in Mail consists of the mailbox list on the left-hand side and the message list on the right-hand side. I don’t have a third pane at the bottom displaying the contents of the currently selected message. I don’t like that, because when that “message area†pane is visible, any message in the message list becomes marked as read as soon as you select it, whether you actually want to read it or not.
People who use Mail in the same way will find the second post especially interesting.
[...] Pierre Igot at Betalogue has some of the sharpest eyes in the blogging world. He repeatedly sees flaws in interface design that I overlook. Whether it is problems with the way Mail handles the format=flowed feature or threading, he’s got it nailed. [...]