Emma,
I disagree. Nadal is one of the few champions who has had to deal with two primary foes at the same time. Although Federer’s peak years were from 2003-2007, I don’t think Federer’s peak years impacted Nadal too negatively since Nadal has never had a particularly difficult time with Federer, on any surface besides indoors. Novak, OTOH has always been the primary foe of Nadal’s and the opponent Toni most feared from the beginning.
If Federer’s peak years were from 2003-2007, that gives Fed five years of peak performance. Nadal is such that people have a hard time determining his prime since he began winning so early. Traditionally, those that peak early, burn out early. So, Nadal has the distinction of beating Federer before his prime, before going on to deal with his most difficult opponent in Novak soon after his own prime began. This has resulted in a ten year period of playing at an extremely high level for an extended period of time.
Federer's best years were from 2003 to 2007 in the sense of peak time, so by the time Nadal finally started exploring outside clay, Federer already had his best years behind him.
I don’t agree that Federer's best years were behind him, because although Federer’s results have tapered off, he still had mastery over Novak and Andy (Andy, particularly in the key matches). Nadal was the only threat to Federer, IMO, during his entire career. I also think part of Federer’s “issues” can be directly attributed to the psychological damage that Nadal has inflicted upon him over the years and has nothing to do with his level of play.
I think Nadal faced more competition than Federer, because Federer was the ATP poster boy and you had professionals being too intimidated to actually play him based on his status in the game. Meanwhile, they came after Nadal like rabid dogs. Roddick, Berdych, Wawrinka, del Potro, amongst others regularly did not give their best against Federer, although with the exception of Roddick, they had the tools to do so.
I don’t give Novak and Andy a pass for their mental shortcomings, because both were equipped with the necessary tools from the onset. The fact that they did not take advantage of some of their prime years lies solely on them.