I see your point. It depends on the type of use you're putting the car through. On a road course where you want quick acceleration coming out of turns, a 4.10 ratio axle gear would be more suitable and especially so if the engine's been cam swapped (less low rpm torque). On the dragstrip, a 3.55 axle gear will allow you to hit the 1/4 mile trap at the top of 3rd gear thus requiring only two gear changes (as in my case) but again, it isn't a case of one size fits all. The combination of performance mods, tire size, transmission ratios, and type of use will dictate the optimum axle gear ratio.
One thing's for sure, the factory 3.31 ratio on 07-09 GTs is way too tall unless you have a positive displacement supercharger, and Ford only opted for that to improve highway fuel economy.