I can only think of two aspects of the 6D that qualify as limitations: the AF system and the frame rate. The frame rate might not be 1DX speed, but it is fast enough to be usable to get great shots, even for sports.
The question is not which one is better. There's no question that the 6D is outclassed by the 5D Mark III and the 1D X. The question was whether it has serious limitations—that is, if there are aspects of it that would prevent someone who knew how to use it from being able to get decent shots. Personally, I don't think so.