I currently have both the Canon and Yongnuo versions of the 600EX-RT. So I have compared, scrutinized, and tried to justify a preference for one over the other and here is what I have concluded. There is a reason that Canons cost more than the Yongnuos and that becomes readily apparent when you actually use both of them side by side. Does the cost difference signify just how much better the Canon is over the Yongnuo? My answer is No! Would I go with a Yongnuo only setup? Maybe if money was the only issue but I really like the Canon 600EX-RT for it's build quality, consistencies and features not found in the Yongnuo version. Yes there are feature differences that just drive me crazy but may not be an issue to someone else. I have listed some below (1-8).
At $120, 1/4 the price of the Canon, the Yongnuo 600EX is a throw away flash in my opinion. Not worth my time and expense to send off to Timbuktu for repair when you consider that for $120 and a 2 day down time (Amazon Prime) I can have a replacement. That is more than likely cheaper and quicker than I can get a Canon 600EX-RT repaired. At that price you can have spares (plural). I am all about spares, one of my compulsive behavioral issues.
I think it has been proven that third party flashes are getting better and offer a very competitive alternative to originals, but cost is not everything. I can't prove it but Canon flashes just seem to be more consistent in flash output, color consistency, ETTL exposure consistency , and consistency between each flash independently. First off they were designed and built to work with each other as well as Canon Cameras in a system that was designed for them. The extra cost of the Canons no doubt comes partly from better quality internal components and better quality control overall which could explain the better overall consistencies from the Canon's when compared to third party flashes. Third party flashes also suffer from reverse engineering issues. There is a reason that most third party flash and radio triggers have a way to upgrade firmware.
If a person does decide to go with a third party flash, it is important that you buy from a company that is reputable and where you can exchange or return the flash easily and cheaply (conveniently). The key to third party flashes is getting a good one from the start as most of the issues, I have read about in forums, were readily apparent upon the first inspection or usage of the flash.
Feature differences between the Canon and Yongnuo versions of the 600EX-RT that are readily apparent to me as I have used both side by side.
1. The Canon flash head tilts and pivots more smoothly than the Yongnuo and locks in the straight forward position. The locking part not the best for bouncing flash but when used in certain situations with certain modifiers it may be an asset (such as "off camera" when a heavy modifier is mounted directly on the flash head). When bouncing flash the smoothness of tilting and pivoting the Canon flash head is much nicer than the Yongnuo which feels stiff and gritty to me.
2. When in Auto Zoom the Canon flash head zooms to 50mm (full frame sensor) when tilted or swiveled to bounce flash where as the Yongnuo will continue to zoom as the focal length changes. If you use Manual Zoom, which I do, then this may not be an issue but it is worth mentioning.
3. The Yongnuo does not have External Metering (Auto flash) but here again not a big issue as most do not ever use this feature (anymore) and probably some that do not even know what this feature is.
4. Not able to remove all the configuration pages, that I do not use, in the Cf. I just want to scroll through 3 pages (Wireless Off, Wireless RT Master and Wireless RT Slave) like I do with the Canon. The least I can narrow it down to in the Yongnuo is these three plus 1 page of the Wireless Optical Slave. Probably not a big deal but to me is annoying and confusing when you are used to the Canon. While we are on Wireless Flash configuration pages there are some pluses and minus for the Yongnuo other than just this one I have mentioned. (see 5 and 6)
5. The Yongnuo does not have Wireless Optical Master capability. Not a big deal if you only use the Wireless RT system but for some crossing over from non RT Speedlites it may be an issue.
6. Since we are on the subject of Wireless configuration pages there are three that you may find in the plus column for the Yongnuo over the Canon but more than likely will never use them. They are Wireless Optical Nikon iTTL Slave and "optical slave" modes (little "o" and little "s") S1 and S2. The S1 and S2 configurations apply to a built in optical slave that will trigger the flash in Manual mode when it see's a flash from another strobe. In the S2 configuration ignores the preflash from an ETTL strobe.
7. There are some Custom function and Personal preference items that are different between the two flashes.
8. Last but definitely not least although very confusing to me. One thing that I find as a "reserved plus" for the Yongnuo over the Canon is the ability to use the Wireless <Gr> mode, with older DSLR cameras, when using the Yongnuo as a Master in the Wireless RT system. I say a "reserved plus" because you can only use the <Gr> mode, with the older DSLR's, in the Manual mode. Yes you heard me right you can use the <Gr> mode with older DSLR's but the groups are only usable in Manual mode and if you try to set ETTL as one of the Group modes it will switch to Manual mode as soon as you press the shutter button.
This is both confusing and disappointing to me because I have really enjoyed using the Yongnuo YN-E3-RT's over my ST-E3-RT's because they allow older DSLR's to use the <Gr> mode just as if you were using an ST-E3-RT with a newer DSLR. All modes are available and usable with the Yongnuo YN-E3-RT with older DSLR's. The <Gr> mode does allow for the ETTL mode to be set and used by a newer DSLR just not an older DSLR when using the YN600EX-RT as a Master. One more thing to mention about the <Gr> mode with the Yongnuo 600EX-RT is that the Ext A mode is not available more than likely dut to the fact that External metering is not a feature of the flash. Probably not a big deal once again because most would either never use it or even know what it is.
I guess my summary of the last paragraph is that if you are using the YN-E3-RT with older DSLR's in the Wireless <Gr> mode just be aware that you will not fully enjoy the same features when using the Yongnuo YN600EX-RT. Basically using an older DSLR with the YN600EX-RT as a Master in the Wireless <Gr> mode is the same as using the Wireless Manual mode but expanding it from 3 Groups to 5 Groups. While we are on the differences between the YN600EX-RT and YN-E3-RT there is no "rear curtain" wireless capability when using the YN600EX-RT as a Master. Just thought I would throw that in here last to brighten your day although the Canon 600EX-RT does not have this feature either.
EDIT: One thing I wanted to add since I have been reminded about it while testing the both the Canon and Yongnuo 600EX's in the hot shoe of the Godox X1, and switching them back and forth regularly. The YN600 is loose in the hot shoe and does not tighten down when you move the lever lock to the lock position (this is the same for all my YN600's). The Canon 600EX tightens in the hot shoe as you move the lever lock to the locked position and it is much tighter in the hot shoe. This has not been an issue as far as connection and communication is concerned but the YN600 does rock back and forth more than the Canon.
Those who mentioned the auto focus assist and the weather sealing, good ones. I totally forgot about those differences but since I have never have, nor will I ever use the YN600 "on camera" I do not pay much attention to those differences but they are important for someone who will.