I guess Nadal's numerous injuries have escaped your attention! that has much more to do with him not holding on to number 1 longer.
and you may think Nadal's game only troubles Federer, but the truth is it overtakes nearly every other player, especially other top players as his winning H2H attest to...
Yes, Nadals peak level of play is amazing. Nobody argues against this. The point is he can't replicate his peak play for longer periods of time.
It's a shame he has injuries. But maybe they are also the result of his peak play.He has to train and play very hard to be able to have such an amazing peak play.
But why should Federer be penalized because of this? He had his share of injures. He also has chronic back problem. But he manages his schedule better and he developed a style for longevity.
All greats have amazing peak play. But the only difference between them and Federer is that he can sustain his peak for longer periods of time. Consistency. That is why he is regarded as the best of the modern era.