Exiting ES takes a while if you have lots of roms and you have used the scraper - see https://github.com/RetroPie/RetroPie-Setup/wiki/FAQ#why-does-shut-down-and-reboot-take-ages
Might be another problem though too - have you tried a fresh image to rule out a hardware issue (power / cabling etc). You could post via pastebin.com or similar the output from dmesg and the contents of /boot/config.txt, /var/log/syslog, /tmp/runcommand.log and ~/.emulationstation/es_log.txt