Big Boss is to battle what Bobby Fisher was to chess, he not only predicts your every move but he likely created the environment that forces your every move.
Falcon is a highly trained soldier, the exact type of mind that Big Boss has grown accustomed to manipulating. Beyond that; Big Boss basically held the entire world hostage with the notion that he could launch a nuclear weapon to any point on the planet from his secret base. All the secret societies, who supposedly control everything, were exposed as they failed in their attempt to take down Big Boss, and -- to my knowledge -- he fooled them into thinking they succeeded.
I see this fight going exactly as Falcon had planned, which turns out to be a plan that was written by Big Boss under the guise of Falcon's commander. A commander gives orders, a soldier obeys. Falcon, in spite of his heroism, becomes a casualty of his devotion.