For anyone watching this thread, the issue has been fixed in recent firmware:

https://community.onion.io/topic/1282/omega2-reboot-and-sd-card-fixed

Everything else, including upgrade, wifi, etc. seems to be working just fine, but the unit will not reboot. It gets to

[ 254.315898] reboot: Restarting system

on the serial console, and then the lights go out, and it never goes any further. Turning it on/off with the toggle switch on the unit immediately causes it to boot back up.

Just to make sure (was pretty sure it wasn't since no sign of messages in dmesg on desktop) I tried powering with an external usb brick instead of via system usb port. Same result - reboot acts like halt.

Any ideas?