When it is snowing out, having the ability to down shift and use the engine to slow the car down with out applying the breaks is a handy and possibly life saving option.
So I vote the manual transmission is better.
Acceleration, Manual wins.
Gas milage, Manual wins.
Increased Driver alertness/awareness, Manual wins.
Increased Break Life (through use of engine breaking), Manual wins.
Fun Factor, Manual wins.
But yes, in stop and go traffic, manual is the suck! Everything has to have a downside :-(