Extra boot files means extra boot time, ok I can admit this.
But.
Here we are speaking about shutdown and not start up.
And if the first boot is slow, or even the second and the third, it's normal. I can figure out the OS needs to update data, create caches, make some basic configuration.
But seriously, after the ten reboot do you find it's normal ?
I'm not speaking about 30 or 40 seconds more, which should be boring but acceptable.
It's may be not a reference for anybody but yesterday I had the time to ligh a cigaret, smoke it and drop it between the shutdown and the Mac totally powered off. With no filevault activated or anything.
This said, I have to admit I just repaired permissions, check disk and launch automated tasks proposed by Onyx (except clearing caches,...) and this reboot tooks me exactly 2min31.
Without opening last session windows and nothing launched at boot.
Just boot, start restart, launch the chrono, confirm and wait for the login window.
So it's already much better.
But I find it kinda weird this need to repair permissions after a "clean" install.
(Installation of OS X Server failed during the migration, so I restore it at the next boot process)