As other people are saying: this match would be very different if only Federer had taken those break points.
This is not a copy of the French Open final. In that game Federer was well and truly outplayed. He didn't stand a chance. He didn't get many break points and he lost game after game after game.
Here that isn't the case. He's two sets down, but he needn't be. He's matching Nadal physically and with skill, but not, as KingEric said, mentally. He's earning himself the break points he didn't gain at the French -- his game is there to the extent he's putting himself positions where he should be ahead. But then he's letting himself down. He's dropping points, shanking the ball out, hitting the net when he should be burying them in the corner and taking those break points.
He's so much better than this, and if he'd only taken some of those breaks then he'd be at the very least on a level playing field here.