Canon 600 EX-RT Cons:
I lost the ability to sync my flashes at 1/400 or 1/500 (Depending on the camera I was using) compared to that standard 5D3 sync speed of 1/200.
No ability to trigger a remote camera
With a 5DIII you can do high speed sync with the RT system (although not with pre-2012 bodies).
You can also fire the camera remotely with from a flash/ST-E3 with another in the hotshoe (pre-2012 bodies can remotely trigger the shutter, but a cable to the N3 socket is needed).
Thanks for the response. I wasn't aware of the remote shutter triggering capabilities, that's something I will have to look into.
On the sync speed, I should have specified; I lose PocketWizard's proprietary HyperSync, which essentially allowed you to fire a full powered flash above your camera's rated sync speed. For me, I was able to get 1/400 on one of my bodies an 1/500 on the other, compared to the standard Canon sync speed of 1/250 or 1/200, which is a pretty big benefit to the PocketWizard system in my eyes. Because both systems can take advantage of Canon's High Speed Sync (Which I use regularly) I don't give a benefit to either solution there.