/usr was the mountpoint for the second drive, where the home directories were. Dennis and Ken started putting binaries into /usr/bin because /bin on the first drive got too full.
See the famous /usr rant by Rob Landley.
Also the idea that everything has to go into a flat /bin directory is nonsense too. My experience is chiefly with illumos, but we have inherited a number of separate trees for compatibility with different standards; e.g., /usr/xpg4/bin had some POSIX binaries where they were incompatible with the default /usr/bin binaries. There were also SunOS (BSD) compatibility binaries in /usr/ucb for a long time. Commonly different JDK versions could be installed alongside one another under /usr/jdk/$version. Unbundled software from many other places would find its way into trees in /opt. Even shared libraries can be installed alongside one another without conflicts, provided you do the right thing with ABI stability and sonames etc.
I have no doubt that other OSes have made a set of similar decisions to provide various levels of binary compatibility and evolution over time, depending on how important it has been to their respective user communities and customer bases.
There is plenty of evidence that /usr used to be the home directories, iirc it was like that in Illumos until 1988.
Edit: Evidence for "user": https://www.youtube.com/watch?v=tc4ROCJYbm0#t=13m40s