May I remind you sir, that Nadal is four years younger than Federer, a pretty large gap in real tennis terms. So in reality there was always going to be a small window of opportunity where they would each other in their prime. Unfortunately due to how bad Nadal was on non clay surfaces early on in his career and even now you see this gap.
May I remind you, that Federer is responsible for almost as many non clay failure to meets? Check out the 2010-11 seasons for example