Nadal leads the h2h based largely on his unbelievable clay court prowess. Likewise his lead in the slams is only so massive because of the 5 French Open matches Nadal has won. Nadal is far more dominant on clay, everywhere else the h2h is alot more even despite Federer declining significantly.
Besides that if you're telling everyone to look beyond the stats you shouldn't just quote numbers of matches won...Federer has had many chances in his meetings with Nadal even at the French. The fact he hasn't capitalised is in part due to Nadal's determination and Federer's mental block against Nadal. In the AO 09 Federer won more points than Nadal, in Wimbledon 08 Federer had 20 plus break point chances that he failed to take. Not only that but Nadal won as the light was fading, big advantage for someone who plays with a bigger margin for error no?