Nadal has a good record against Federer for a reason most people, I think, don't notice. Since Federer was No.1 and Nadal No.2, Nadal had not been good enough in hard court events, until the last year. Since they're always the top 2 seeds, they can only meet in the final of a tournament. In in those years past, Nadal had not been good enough to meet Federer in hard court finals. However, Federer had been the second best clay court player since Nadal became the king, so have had many occasions to meet him in clay court finals, and obviously, he lost most of them to Nadal.
So, this is really why Federer has a bad record against Nadal. It's because most of their meetings were on clay, where Federer just could not beat him except on a couple of occasions. And Nadal, until now, was not even able to meet Federer in the finals of other surface tournaments, save for Wimbledon.
Well, we'll see how long Nadal can play. Not as long as Federer, for sure. His game is too harsh on his body. He is this young, and already having problems. But no denying he is also one of the real greats of the game.
This sum it all.