I think the difference is that Nadal is more of a grinder, he doesnt look to close out points early on. He would rather wear you out and wait til you miss. Playing that style of game is hard on your body.
Fed, on the other hand, is more of an all court player. He will close in on the net and take advantage of a short ball. He will serve and volley some to make the points short. Therefore, his points and matches dont take as long, not as many shots and chasing balls down. This style of play is way easier on the body. Think about reducing each point by 1-2 shots, and then multiplying that by an entire 4-5 set match, then multiply that by 4-7 matches a tournament. Thats a lot less running and chasing.