When it comes to clay, Nadal is a player of another caliber. It can be argued that Federer is the world's second best clay court player, but you would never know it today. He faired better on the clay court ATP tour but today he was just simply out-classed and it was painful to watch. Too many unforced errors, no back-up strategy and just being sinply out-played. You'd think Federer would've studied the last three years of videos of R. Garros finals/semi-finals, and try to figure out how to beat Nadal; in turn he was beat by a player who's clay court game is nearly flawless.
Concerning other surfaces, I think Nadal is breaking through at least on grass; he was in the final with Federer last year at Wimbledon.
edit to say that even Djokovic gave a more challenging match to Nadal than Federer did in the final