Naked Snake/Big Boss
I name the original Snake over the clone because he's demonstrated how awesome he is countless times.
He takes on a team of super soldiers and wins, he keeps the cold war from escalating a number of times, he kills his own mentor and can never really get past it, he's lost his eye and came back more determined than ever, he starts his own army, and that's just to name a few examples.
The guy really is a one man army. I may not like Peace Walker's story, as it was rehashing plot points already developed in MGS3, but it is a damn good demonstration of just how unstoppable Big Boss is (though MGS3 is, as well).