My only experience with the 5 speed is a short test drive at the factory with a 5 speed demo unit. Our 6 speed seems a little quieter when starting from a stand still to cruising speed and also not as much noise when downshifts are required. The tow/haul mode in our 6 speed when descending 8,10, and 12 percent grades in the western mountains sure saves a lot on brakes.
Also, if I remember correctly the 6 speed also has a somewhat different transmission fluid filtration/circulation system that extends the fluid change out interval. I don't have those documents currently available to confirm this so anyone interested should search out the appropriate literature or ask a Ford Dealer.