Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
Some Apps may be to blame

I upgraded from SL to Lion and saw the slow shutdowns being reported. After uninstalling Fan Control and Techtools Pro 6 the shutdown returned to the normal 2-3 seconds. Look for applications that you installed that hav'nt been updated to support lion.
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.