On transferring the data/hdd from the old mbp to the new, I also transferred the slow shutdown speed as well and decided to see if I couldnt do something about it or at least determine the cause.
I checked under console and saw that one of the last things that it was trying to do was to allow parallels to close down its network connections etc, so I decided to try uninstalling parallels and see if that made a difference.
Unfortunately in order to uninstall parallels I first had to update it to the current build so that the uninstaller would work, which required a couple of reboots but even after it was uninstalled, there was no change in the shutdown time.
So back to console and this time I notice a message that the EyeTV helper failed to quit, so I went into activity monitor, quit it manually and tried the shutdown process again and again it took around a minute.
Im going to go have a look in the console again now but I'm really curious what could be causing this...