Nadal will most surely come away the winner except on grass (where balls won't get high up and Fed's weakish bh drive becomes a weapon). It probably will be like Navratilova-Evert rivalry in the early the 80's.
Nadal is really the kryptonite for Federer. He takes advantage of all the minor imperfections in Fed's game: a backhand that can be short and tame when hitting heavy and high topspin balls; a forehand that can go awry when pressing, which happens when somebody keeps retrieving his corner shots or he is frustrated that he can't get into his float-like-a-butterfly-and-whip-and-flick-winners-all-over-the-court mode; lapses in concentration especially after an easy first set; fitness problems in an extended match (think of how short his matches usually are and what a poor record he has in 5-setters, Nadal hasn't taken advantage of this problem yet).
Whoah, calm down dude. They've only played 5 times, all were close. A few points here & there decided the outcome.
I think Fed would have won had he won the 4th set. He had the momentum. His fitness looked fine after 4 sets(& it was 3:40) Nadal looked a bit weary.
Nadal's fit, but not really sure how fit. He hasn't played that many 5 setters & it is very exhausting to play that style of play. And he's so young. Most guys hit their fitness peak a bit older(22-24), like Lendl, Muster, Courier.
I don't think Nadal is obsessed with being in the gym all day like those guys. He may get that way later.
Courier was a heck of a lot fitter than Sampras, but Sampras won way more 5setters. 5 sets isn't about fitness all the time, but your mental toughness & ability to win big points. And Sampras played a less physical game than Courier, he conserved energy throughout the long matches.
Fed plays such a relaxed, easy game, I think he could do well in 5 setters. He plays so few of them, though.