I think the point is that not many finals that Federer lost were played out in Federer's prime of 2003-2007. In fact, I count only 4 total finals between these two, with 2 Wimbledons to Federer and 2 French Opens to Nadal.
What would have been interesting is if Nadal was the same age as Federer.
That is one of the main reasons we cannot compare different eras. However, I disagree about Fed's prime. How about 2009? Did he not win 2 GS and reach the final at the other 2 GS? Looking only at one's "prime" years is silly IMO.