I have the same issue on my MBP 2012 Retina.
Can't shut down nor restart (unless manually) -- ALSO, certain USB devices don't work. My superdrive and USB Blue Yeti mic don't work, however external drives DO work, strangely.
I've done 4 re-installs. Reset P Ram, SMC, etc.
Talked to 3 agents by phone on Apple Support. Taken it to Apple store for a complete reformat and reinstall.
The same problems remain. Everyone is stumped.
Based on this thread, this seems to be a known bug.
Except I have the extra headache of USB malfunctions.
So very, very, very frustrating. Any other ideas?
My thread: El Capitan Bugs: USB Ports Not working + Shut down / Restart Problems