REPOST from another thread for your reference:
I finally had a chance to compare both my bodies (5D3 and T1i) with two flashes (600EX and 430EX II). I used the 40mm f2.8 for both (at first) with center point selected to keep things as consistent as possible. I shot into my walk-in closet, so it was dark enough to trigger the AF Assist light but with the door open so some ambient light would trickle in. I turn the focus confirmation beep back on to have another indicator of when the camera thought it was focused and when it fired. I tried both cameras with both flashes. I did not time anything with a watch because if it's close enough not to be able to tell there is a significant difference, I really would not be bothered which one is technically faster. That said, here are my observations:
5D3--regardless which flash used, the body had the marked hesitation that I mentioned earlier/elsewhere. This is not just a little shutter lag--this is a full second or two, the moment is gone, I didn't get anything and, if I did, it is not in focus. This is beyond annoying, this is failure when mission critical. There was no perceptibly meaningful difference between the flashes, so this lead me to believe it's the way the body acquires focus. I noted the two or three step confirmation process someone noted earlier. This was the behavior no matter which focus point or AF method was selected (excluding SERVO).
T1i--press, shoot. Find another spot, press, shoot. Repeat, Repeat. All in focus, all virtually instantaneous and at worse considerably better than the best attempts with 5D3. If anything, 600EX performed better than 430 EX II (thank goodness for that) on this body. This is what I was expecting from the 5D3 and it's not even close. (I repeated the test with my 15-85mm zoom on the T1i and the results were consistent regardless of the focal length and aperture setting).
I'm now even more convinced it's a serious with the 5D3 and not the flash. There is no way my T1i (which I still love) could/should outperform the 5D3 under these circumstances, especially given the type of photography the 5D3 is geared toward.