The original history behind a lot of original UNIX directory structure is engineers running out of disk space on a PDP-11 50 years ago and shuffling things around to keep the system operating. Other reasoning has been piled on top over the years.
A lot of thoughts [1] have been put into the usr merge, and compatibility with unix is one of them, and one other unix that has done this merge is Solaris, so Linux distros doing the merge are not even that special.
