I own 6 x 600EX-RT and 2 x YN600EX-RT. I also own 1 each of the Canon and Yongnuo transmitters. The Yongnuo flashes are indistinguishable from the Canons in about 95% of applications. The Yongnuos are about a stop less powerful, according to my light meter, measuring output from both at a standard distance and at various zoom lengths. Maybe 2/3 if you're being really generous. Either way, they make great backups or when used to gel backgrounds/small background objects. They also make a great on-camera fill while controlling a Canon off-camera.
I don't like the YN non-locking swivel aspect. The hotshoe locking mechanism is VERY MILDLY less well built and/or fitting than the Canon as well.
As far as RT operation, I've only ever had one issue with the YNs and the RT network. That was the first night I used them, the day after getting them, and employing them in a 10 light setup (my 8 + 2 borrowed Canons) to light several Porsches. I had an intermittent issue with the 2 YNs falling off the network and not flashing. I still haven't figured out what was happening that night. And I've used multi-light setups with the YNs involved since then and not had a single issue since that first night. Bottom line is that they play seamlessly with the Canons, and with either transmitter. If I didn't tell someone they were YNs, they would be none-the-wiser.
I do like the Yongnuo transmitter better ONLY because it has IR focus assist. For the life of me I can't understand why Canon could not include that in their transmitter. It is so much lighter to mount the transmitter than having to use a non-firing flash in the hotshoe just to be able to use focus assist.
If I were an amateur just looking to take advantage of the freedom that the RT flash system provides, I'd go for 2-3 x YN600EX-RT and the Yongnuo controller. You'll still come in well under the cost of a single Canon 600EX-RT, and have a complete solution. You'll likely never notice what you would be missing with the Canons. And if one happens to fail or break, it's a hell of a lot less painful on the wallet!
As a working pro, I need the dependability and CPS backup of having the Canons as the basis for my "small lights" kit. I use the Yongnuos as backups and in the rare occasions when I hit a venue or job that needs a couple of extra lights for best coverage. I have done 2 "light" setups with four flashes in each "light" mounted on Foursquare brackets in 48" and 20" softboxes when shooting outside.
One thing I haven't specifically tested is any difference in the overheat protection operation. I often use a Foursquare mounted four-flash setup with battery packs to shoot sports outdoors. In the summer I'm finding I can start hitting the overheat protection slowdown on the Canons about 100 runners into a race. They work great in cooler weather, but 90+ degree heat makes this setup untenable for larger, fast paced events. IF the Yongnuos are less overheat sensitive, that would be a plus. I should check that out. But then again, I just invested in several Profoto TTL/HSS lights so the point is moot to me now. No overheat issues with the Profoto B1s or B2s. Now I just have to spend $$$$$ for more batteries. :-[
Hope that helps with the Canon vs YN decision....from someone actively employing both in paying work.
