Perfectly natural for an 18 year old to run out of gas in a 5-setter. IMO, it would be very stupid to change his game so that it lasts longer, especially if it means putting less top spin on the balls... that's his weapon!!!
He could and should
have beaten the number one in 3 sets on a surface that's not even his favorite. If he learns how to finish the game quicker (match length, not rallies), he wouldn't even need to worry about his fitness.
Anyway... who are supposed to be the fittest men in tennis? Clay players. What tactics do these players use? Top spin and running down balls. Pssst... I'll let you in on a little secret: clay court players are fit because of their tactics
... Nadal isn't quite there yet fitness-wise (logical), but the tactis he uses and the court he usually plays on will just give him a further incentive to work on that. In a couple of years he won't have any problems with 5-setters and that without changing his game.