No one is discarding the win, everyone is just saying that the sample is too biased to be used as a true indicator of who is the better player.
Strong knowledge of basic statistics in this thread.
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.