I think that auto or manual is mostly a matter of personal preference, and some of what you want to do with it.
I believe that autos (Provided that the transmission can handle it) will be faster on the quarter mile, particularly with turbocharged engines if for no other reason than the fact that it doesn't let off boost in order to shift. I believe that autos are somewhat more trouble on road courses, due to being unable to select the gear when you get back on the gas at the corner apex.
The most cost efficient transmission is the one that's already in your car, unless you've managed to reduce it to a heap of scrap, and then it's probably still more cost efficient to replace it with another similar one.
That said, it's probably more cost efficient to swap a manual into an auto car, rather than buy a different car if a manual is what you want.