I think the "massive problem" has to do with the recovery included in the KitKat package.
I downloaded the OTA from a thread on XDA. After following Jcase's instructions for SlapMyMoto to maintain root after the upgrade, I copied the OTA zip file to my SD card and rebooted to recovery. After running "install update from SD card," the phone rebooted to recovery.
As most probably know, the recovery screen just shows Android triage (the green android on its side, with an access door open and the red triangle with an exclamation point). You have to hit power and volume+ at the same time to get the recovery menu, including "install update from SD card.
After installing the update.zip a second time, the phone booted to KitKat. I followed the remaining steps for SlapMyMoto and am now running 4.4 with root.
I'm sure lots of people took the OTA, then saw the triage screen and thought their phones were bricked. I think just entering recovery and installing the update a second time would solve those problems.