iMac not shutting down since upgrading to OS X 10.11, El Capitan
I have found that clearing all cache and font maintenance resolved the issue.   

rm -rf ~/Library/Caches/*
rm -rf ~/Library/Saved\ Application\ State/*
sudo rm -rf /Library/Caches/*
sudo rm -rf /System/Library/Caches/*
atsutil databases -removeUser
sudo atsutil databases -remove
sudo atsutil server -shutdown
sudo atsutil server -ping
sudo rm -rf /var/folders/*


Restart immediatly