If Nadal plays his best on clay, he's going to beat Federer on clay. Sure. But if Federer played his best on grass, he wouldn't have lost the '08 Wimbledon. He is, after all, pretty much indisputably top-2 on grass all-time.
But I think its silly to blame all of Nadal's losses on injury or being tired. Come on. But even so, his injuries are all related to his style of play. Some of his losses -- also inability to defend Wimbledon -- were due to injury. Not the case everywhere, though. Madrid is a 3-set tournament; I don't think his SF against Djokovic played that much of a role in his loss. What happened is that Federer was rejuvinated and playing exceptionally, and employed new and effective strategies against Nadal on clay. Nadal wasn't at the top of his game, and thus lost.
A similar explanation is valid for Federer's AO and USO losses, although I don't think DP or Nadal employed any new strategies. They just played very well, and Federer had awful serving days on both occasions.
When Federer plays at the top of his game, no-one is going to be able to beat him except Nadal on clay. Same for Nadal on clay, no-one's going to beat him on clay if he plays his best.
As for longevity, I still think that Federer will outlast Nadal. From what I can tell, Nadal seemed to peak from mid-2008 to early 2009. That was his best period. Despite that being his peak, I still think he benefited from Federer not playing his best at Wimbledon (although there Federer did play very well), and serving awful at the AO. None-the-less, Fed wouldn't have beaten Nadal playing his best at this year's FO either; it happens.
None-the-less, Nadal had a peak from mid-2008 to early-2009. Then his body gave out. Unfortunately, I don't think he'll be able to get back there, unless he makes significant changes to his game.