Right, because we should expect that, as Federer leaves his prime and Nadal enters his, Federer's record against Nadal will improve?
There is no question that Nadal is a difficult match-up for Federer, especially on clay. However, in his prime, Federer beats Nadal in GS outside of clay. And it likely wouldn't have been any different if Nadal made the USO and AO finals from '04-'07, as grass was Nadal's 2nd best surface (hard his worst), and he couldn't beat Federer there.
It boggles the mind how some people can say that Federer isn't the greatest player of this decade. He has 15 slams. Nadal has 6. That's Federer with almost 3 times as many slams as Nadal this decade. Clearly, Federer is the best player of this decade, it isn't even a question. #1 ranking too, 4 straights years #1, now adding to # non-consecutive weeks #1. No-one has spent more time as #1 in this decade.
Nadal is an incredible player, and it's really remarkable that 6 of his 6 Major wins have come over Federer. However, the reason he's such a difficult matchup for Federer is also the reason his knees are betraying him. So it isn't "unfair" that he has to deal with the consequences of his style of play. It wasn't "unfair" that he lost at the FO or couldn't play at Wimbledon. It was a consequence of his style of play. Now, look, it's too bad that he got injured, of course. But it isn't like it was something that was bestowed upon him by random chance.