H2H is not only indicator but is main who is better player by my opinion.
Especially in case where one player is younger than other , we all know that all older players should get at least 5-6 easy wins against younger player in his early years. Especially if the name of older player is Fed - best one in that time.
Simply Nadal is better than Federer because he is able with his grinding defense to absorb all Fed attacks and to force him to make UE or hit winner from defense.
So are we going to ignore natural disadvantage Federer already has with his one hander? This difference is easily exploited on clay where the ball bounces higher and surprise, surprise, most of their meetings have been on clay. Keeping this in mind, is it even a surprise that Nadal leads H2H?