Same reason, since you won't have shut down all applications unless you are in the habit of killing all processes in the activity monitor. There's a process (or processes) somewhere, written by a clueless **** or otherwise, waiting for an event to occur before it shuts down.
What about after clean installs? I did three clean installs of Mountain Lion and after every single one I had slow shutdowns. All three installs were on a mid 2012 retina MBP 15. I made sure all updates were installed and did multiple shutdowns without installing anything or setting up iCloud and I still had slow shutdowns.