As I recall, it has been proven that the '05 GT can hustle around a road course faster than an '03/'04 Cobra. That would mean it has a better suspension and possibly better brakes. And the difference at the 1/4 mile track isn't as bad as it used to be (until the GT500 drops). Yes, the '05 GT is heavy, but the '04 Cobra is heavier still.

The '05 GT is making ~320HP (in reality) on those non-forged internals. And since it doesn't use forced induction, it doesn't need forged internals. I can't really see how the number of cogs in the transmission makes a significant difference. The 400HP Pontiac GTO has 6 gears, too, and the GT still runs door-to-fender with it 0-60, and no more than two cars back in the 1/4.