Grass is a surface where big servers and powerful strikers of tennis ball can take you out on their best day. The margins are very small in grass. Federer dominated grass in his peak having a 65 match winning streak and 5 titles in a row. The declining of federer federer prime was 2010 where he had shocking losses. So more of those losses you have mentionef came when Federer was in his 30s. All those matches were close ones which Federer should have won except that Berdych match where he was outpowered.Nadal except his 2015dal form has been only beaten by Soderling, and even that was no really Peak Nadal (exhausted from his insane clay court season)
While Federer has been beaten fair and square by Nadal, Djokovic (3 times in finals), Berdych, Tsonga, Sthakovski, Raonic, Henman and Anderson.
Federer on grass has his ultimate serve and variety
Nadal on clay has his ultimate topspin FH.
Nadal is really stronger than Federer or because Federer had more competition ? Nadal is still dominant as ever at Roland Garros with his physical game at 35, while Federer with his more economical and complete game at the same age couldn't defeat Djokovic and Anderson.
The surface is more relevant too. Grass reward first strike tennis and variety while clay reward defensive abilities and topspin.
Nadal is better than Federer or the clay surface is the most difficult to earn ?
On clay big hitting guys are hardly a threat as the slowness of the surface gives enough time for Nadal to defend. On the otherhand no one else plays the game that Nadal does on clay. So basically Nadal doesn't had much threat as there are no clay specialists who can defeat him at his own game.