Nadal is without doubt the best clay courter ever to play the game. He is virtually unbeatable on his day, as evidenced by his record at the French Open. While it could be said that Federer probably should have beaten Nadal on clay a little more often, it's very difficult to hold it against him. There isn't a player in history who could live with Nadal on the surface. He's a freak of nature. When you consider that 12 of Federer's 17 losses to Nadal have come on clay (let's face it, were it not for Nadal, Federer would have won the French Open as regularly as he won the other grand slams), it's not hard to see how their head-to-head record falls so heavily in Nadal's favour.
When you look at their record on other surfaces, it's much more competitive. Federer actually edges it. That's not to undermine Nadal's achievements - precisely the opposite in fact. To have achieved what he has is quite remarkable. Indeed, he may well go on to be acknowledged as the greatest in the future, but what's important to remember is that we're talking about two of the greatest players ever to have played the game, not one. So holding Nadal's victories over Federer as a means of undermining his achievements really misses the point. They are both phenomenal.
Anyway, I'm pretty sure we've had this discussion before, and I made my case about as clearly as I could then. It just amazes me that people are still so quick to undermine Federer, when he has played such an integral part in raising the standard of men's tennis.