I think Federer can't match Nadal's intensity--mentally or athletically and that intimidates him. The intimidation then causes Federer to choke and go out of the game plan he needs to win which is coming into the net. I also think that Federer lets his ego get the best of him when he plays Nadal. Federer tries to prove to Nadal that his backhand is not vulnerable so he continues to hit topspin even when it's not working; he also let's his ego get the best of him when he tries to beat Nadal at Nadal's own baseline bashing game. It's reminiscent of Becker trying to battle Agassi from the baseline rather than play his natural serve-and-volley game.