Apple - Rebooting machine with macOS Sierra takes very long time

I had the same issue and it seems to be fixed when upgrading to MySQL 5.7.15

Cheers

Ok, I've found the solution: mysqld is the problem, version 5.7.13 can't be stopped (even from Activity Monitor or with kill), so macOS waits for it to stop until a very long interval.

Solution: Untick automatic startup in MySQL preference pane, reboot once slowly, then the second reboot will be fine.