Another poster said this, but I will as well: While Nadal does have titles at both hardcourt majors, he's only made the final one time in each of those majors. While I will never be one to say this, some people could argue that those titles were a fluke if he never makes it to another final or a win, especially the USO since he didn't face (in my mind) a truly difficult opponent till the final.
After all, Federer does have 3 finals to back up his Roland Garros win, and it could be very convincingly argued that Nadal is the only thing standing in his way of 21 or more majors. Realistically, Federer has performed at a very high level no matter the tournament, and consistently high levels at all tournaments. Nadal has never shown Federer's level of hardcourt dominance with the grass dominance, and near dominance on clay (hell, the guy was the second best clay court player for 2-3 years, only ever being stopped by Nadal himself, so realistically no Nadal= total Federer domination for 3-4 years)
Nadal has shown a serious ability to dominate on clay, but not any other surface (he's successful at wimbledon but doesn't always back that up at queens, though Federer most definitely does at Halle)
In my mind, Nadal has to dominate, and show consistenly top tier results for several years to come. This was his best year, I think, in terms of w/l ratio, and I believe that Federer's had two or three seasons with a higher ratio.. So while Nadal's performance in the majors mirrors that of his Rival, Federer dominated the whole season in a way that Nadal hasn't, and may never, do.