For anyone that says Nadal is better than Federer (I assume this is meaning in terms of greatness and not just as a matchup) due to the head-to-head, do you also have Davydenko above Nadal on hard courts due to his incredibly favourable 6-1 head-to-head on the surface?
I would find that absurd given that Nadal has 2 Majors (from 4 finals) in comparison with Davydenko's 0 Major finals (and only 2 SF) on hard. This is before you even add in that Nadal has the Olympics on hard, more Masters, more titles and more finals overall on the surface.
Likewise, I find it absurd at this stage to put Nadal over Federer when Nadal's 2nd best Major (Wimbledon - 2 titles from 5 finals) is only slightly better than Federer's 4th best Major (Roland Garros - 1 title from 5 finals). This is before you add in Federer's vastly superior record at the YEC and more weeks at #1. Nadal has the Masters record, which is part of the reason why he is the best ever player on an individual surface.
There is no doubt that the matchup with Nadal has hurt Federer's legacy. In that he has not won numerous titles that he could have added to his collection. That is what matters at the end of the day.
Nadal could eventually eclipse Federer's accomplishments, however I do find that unlikely.