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Hmm, I had the opposite results: my 50 1.2L focused a lot faster than my 50 1.4. I don't use a 6D so maybe it's different but my EOS 3, 5D2 and 7D all drove the 50 1.2L faster than the 50 1.4. Of course, perhaps that's splitting hairs as they're both pretty slow compared to even a slow normal zoom like the 24-105 L.
Oh, then it might be the 6D. Actually, I used the 50mm 1.4 on both a 1D mk II and a 60D but not the 6D. So I actually did not compare the 50L and the 1.4 on the same body... so you might be right. Anyway, this is quite subjective and as you say both are quite slow to focus.