Nadal has almost 2 times wins against Fed than he does against him.
I can compare all this with boxing.
For example I am Lenox Luis , and in my prime years, there is no any boxer who can beat me and because of that I get numerous titles. After some time new young boxer comes , for example Vladimir Klitchko and he kicks my ass dozen of times.
Does all my titles won mainly against weaker boxers makes me better than he ? I think not....
H2H is more important. Especially between champions.
Nadal is the undisputed champion on clay: 12–2 H2H. On hardcourts and grass it is more even: 6–5 and 2–1 to Federer.
Even if Federer had won all their matches on grass and hard, Nadal would still lead the H2H, because he is so dominant on clay.