I think it is ridiculous that the same argument keeps coming up.
If you take clay out of the equation, I believe Roger has a winning or even record against Nadal.
2004 Miami R32: Rafael Nadal def. Roger Federer (6-3, 6-3)
2005 Miami F: Roger Federer def. Rafael Nadal (2-6, 6-7, 7-6, 6-3, 6-1)
2005 French Open SF: Rafael Nadal def. Roger Federer (6-3, 4-6, 6-4, 6-3)
2006 Dubai F: Rafael Nadal def. Roger Federer (2-6, 6-4, 6-4)
2006 Monte Carlo F: Rafael Nadal def. Roger Federer (6-2, 6-7, 6-3, 7-6)
2006 Rome F: Rafael Nadal def. Roger Federer (6-7, 7-6, 6-4, 2-6, 7-6)
2006 French Open F: Rafael Nadal def. Roger Federer (1-6, 6-1, 6-4, 7-6)
2006 Wimbledon F: Roger Federer def. Rafael Nadal (6-0, 7-6, 6-7, 6-3)
2006 Masters Cup SF: Roger Federer def. Rafael Nadal (6-4, 7-5)
2007 Monte Carlo F: Rafael Nadal def. Roger Federer (6-4, 6-4)
2007 Hamburg F: Roger Federer def. Rafael Nadal (2-6, 6-2, 6-0)
2007 French Open F: Rafael Nadal def. Roger Federer (6-3, 4-6, 6-3, 6-4)
2007 Wimbledon F: Roger Federer def. Rafael Nadal (7-6, 4-6, 7-6, 2-6, 6-2)
2007 Masters Cup SF: Roger Federer def. Rafael Nadal (6-4, 6-1)
2008 Monte Carlo F: Rafael Nadal def. Roger Federer (7-5, 7-5)
2008 Hamburg F: Rafael Nadal def. Roger Federer (7-5, 6-7, 6-3)
2008 French Open F: Rafael Nadal def. Roger Federer (6-1, 6-3, 6-0)
2008 Wimbledon F: Rafael Nadal def. Roger Federer (6-4, 6-4, 6-7, 6-7, 9-7)
2009 Australian Open F: Rafael Nadal def. Roger Federer (7-5, 3-6, 7-6, 3-6, 6-2)
2009 Madrid F: Roger Federer def. Rafael Nadal (6-4, 6-4)
2010 Madrid F: Rafael Nadal def. Roger Federer (6-4, 7-6)
2010 World Tour Finals F: Roger Federer def. Rafael Nadal (6-3, 3-6, 6-1)
2011 Miami SF: Rafael Nadal def. Roger Federer (6-3, 6-2)
2011 Madrid SF: Rafael Nadal def. Roger Federer (5-7, 6-1, 6-3)
2011 French Open F: Rafael Nadal def. Roger Federer (7-5, 7-6, 5-7, 6-1)
2011 World Tour Finals RR: Roger Federer def. Rafael Nadal (6-3, 6-0)
2012 Australian Open SF: Rafael Nadal def. Roger Federer (6-7, 6-2, 7-6, 6-4)
2012 Indian Wells SF: Roger Federer def. Rafael Nadal (6-3, 6-4)
In Grand Slams, Federer has a terrible record from the FO against Nadal.
Nadal is a great player. He isn't, however, Roger Federer. He won't reach him in slam count, and won't ever be as good as Roger was across all surfaces.
I mean realistically, Roger is the second best clay player of all time, and the best on every other surface.