Slow reboot after upgrading to OS X El Capitan
Here are few suggestions to troubleshoot the slow reboot issue:


After the system is booted, run:

sudo dmesg | less


and check for any errors.
Start up your Mac in safe mode (hold Shift after restart).
Start up your Mac in single-user mode (CMD-S) or verbose mode ( CMD-V).
Check for any suspicious messages in /var/log/system.log file during boot time. Or use the Console.app to check the logs during boot time.
Check the health of your battery using an app.
If you got any system crashes, please check for any shutdown causes.
Disable non-Apple kernel extensions (check by kextstat | grep -v com.apple).
Disable non-Apple services at startup (check by launchctl list | grep -v com.apple).
Make sure you don't use any custom boot arguments (check by nvram boot-args).
You can consider booting in verbose mode by: sudo nvram boot-args="-v".
Run Apple Hardware Test on your Mac (hold the D key during on reboot).
Book an appointment at Genius Bar and ask them to run the full hardware test using their macOS NetBoot Triage Image.