I have kinda the saaaame problem..
Sometimes it shuts down "properly", it only takes 10-20 seconds, before used to take only 2-3 secs..
But most of the times, it takes for ever.. It actually never shuts down. It only shows the desktop background and all the apps in the bottom and it stays there.. I have to shut it down manually or it would never do.. I guest I would have to do a clean install or I dunno... I never had parallels so that's not the problem.
I have MacBook Pro Retina 15'' early 2013. It still working pretty fast with most of my apps like photoshop and maya.
I'd love to do a clean install but I just can't atm, I'm full of work.
Also, I practically never shut down the computer, it's almost always on. But sometimes I've to do a quick restart, and it takes forever cuz never shuts down...
Any solution?