You're right. All Cortex A9 chips are the same. What might differ is the fab process. A company could make it at 40 nm, another at 32nm and another at 28nm, so you would get further optimization from that as well.
Apple's A5X SoC is 50% bigger in surface than Tegra 3. Considering the Tegra 3 SoC contains 4 CPU cores, and Apple's A5X only 2 CPU cores, plus taking into account all that extra space, I could see how A5X's GPU easily doubles Tegra 3's GPU in size, if not more. That's where the performance increase is coming from. Hopefully Nvidia and others will be smart enough to build bigger chips with in the next generations.
Apple's A5X SoC is 50% bigger in surface than Tegra 3. Considering the Tegra 3 SoC contains 4 CPU cores, and Apple's A5X only 2 CPU cores, plus taking into account all that extra space, I could see how A5X's GPU easily doubles Tegra 3's GPU in size, if not more. That's where the performance increase is coming from. Hopefully Nvidia and others will be smart enough to build bigger chips with in the next generations.