You're assuming that there are options (if buying new)!
More and more of the true sports car assemblers are pushing to have one version only - typically a man-u-matic, ala Tiptronic. The costs are becoming too great to offer so many versions of one car. It's trickle down and crawl up. The econo boxes are typically only 5 speed manual...
If you look at real world numbers, man-u-matics and manuals are almost equal in practically all performance aspects. Even track times are faster for man-u-mats when the driver's are too. (F1 has been man-u-matic for what, a decade?) However, I know for a fact, that few drivers can compete with the accuracy and speed of man-u-matics. In fact, one Italian assembler had to
slow down the shift times of it's road cars because customers complained that they could feel the shift....
If given a choice of auto, manual or man-u-matic, I'd go man-u-matic. Based on European traffic alone... and my quads get enough work out in the gym.
Oh, and BTW - This coming from someone who believes that the only real Ferraris are front engine and 12 cylinders.....