Ubuntu MATE 16.04 restart/shut-down halts due to a not responding program. How to stop it?
This seems to be a regression of this bug:
https://bugs.launchpad.net/ubuntu/+source/unity/+bug/729827
So, the workaround (provided you dont need assistive technologies) would be:
sudo mv /usr/lib/at-spi2-core/at-spi2-registryd /usr/lib/at-spi2-core/at-spi2-registryd.old
This renames the file for at-spi2-registry so that the system won't run it, but maybe you also want to reopen it on launchpad.