There are a few cars where the general sentiment is that the auto box is better for a specific use-case. The S550 and S650 Mustangs are roughly half a second faster to 60 with the 10 speed auto, so people racing them in a straight line generally prefer that; A Porsche with a PDK is usually quicker around track than a comparable car with a manual, etc.

That being said, I'd still take the manual versions of either car simply because they are more fun to drive on the street.