The problem isn't that Nadal owns the H2H. If Nadal is the better player and simply beats him more, then that's just how it is. The problem is that Federer in fact is the better player. He should be ahead of Nadal in H2H, but when he plays against him, he just folds. He gets a weak scared look on his face. That's the problem folks.
*Not counting yesterday, since he clearly had back problems.*