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

I also had this problem and I spent about an hour on the phone with Apple. It turns out that there was an issue with a 3rd party application.

Once i went into System Preferences > Users and Groups> then into Login Items and deleted all of the items in the list, my computer was able to shut down properly.

If you use Avid products you might try removing:

/Library/Audio/Plug-Ins/HAL/Avid CoreAudio.plugin/ 

or

/Library/Audio/Plug-Ins/HAL/Digidesign CoreAudio.plugin/ 

this was the cause of three of our computers not shutting down after the El Capitan upgrade. After removing the first shutdown will require sudo shutdown -r now from the terminal or press and hold the power button. This solved the problem for all three computers for us.