I am a Campagnolo fan and have run it for years. I have Super Record 11 on 3 bikes and Chorus 11 on another. But in this case, I would actually go for Shimano.
Ultegra is a newer groupset and will remain current for longer. I can see Campagnolo ditching Centaur soon now that 11 speed Athena is out there. Also, the Shimano wheels will be better than the Khamsin. Much lighter, and less esoteric. And, carbon or otherwise, the Ultegra chainset is stiffer and lighter than Centaur.
How about Athena 11 with alloy cranks and Fulcrum Racing 5/3 wheels depending on the budget?
In the end there isn't much to choose. Both are good, but Shimano just edges it. In fact, it's so close that it's worth considering what frame you are putting it on and what just feels right. What's the frame?