Thanks a lot man - situation was similar on my 2011 iMac. Not quite as bad as 2 1/2 minutes, more like 1 minute or so, but surely annoying. Whereas the MBP 13" shut down within a finger-snap after the Yosemite installation and significantly faster than with Mavericks.
Apart from Parallels leftovers there was also other residue from uninstalled programs in the Launch Agents and Launch Daemons folders. Deleted all that and also some Parallels junk in the Preferences folder. Additionally trashed my Cache folders and repaired volume permissions.
Now the iMac shuts down within a few seconds too. Once more, thanks a lot. I hope someone at Apple has already moved this solution into the Yosemite troubleshooting knowledge-base.
Note: it's not always Apple who are to blame if something goes wrong with their computers. Unfortunately there are a few too many sloppy software developers out there and it really seems as if the days of living without the need for uninstall utilities are also over in Apple-land...