Rafael Nadal smashed Roger Federer 6-1, 6-3 in the Italian Open finals, improving his record against Federer to 20-10 overall and 14-6 in finals. No one consistently outslugged Babe Ruth in Ruth's prime, no one consistently outgained Jim Brown in Brown's prime, no one consistently outplayed Wayne Gretzky in Gretzky's prime and no one consistently outplayed Michael Jordan in Jordan's prime. Ruth, Brown, Gretzky and Jordan are widely considered to be the greatest players of all-time in their respective sports and--even though there are other valid claimants to the throne in each sport--those players clearly dominated their own eras. Roger Federer has been called the greatest tennis player of all-time, so it is jarring to see him repeatedly not just beaten but often dominated to the point of humiliation by Rafael Nadal. If Karl Malone had outdueled Michael Jordan in the 1997 and 1998 NBA Finals instead of the other way around then Jordan would still be considered great but he would not be the icon that he is now with six titles in six Finals appearances.
Federer's advocates like to point out that a big part of Nadal's head to head advantage stems from his 13-2 record on clay versus Federer but (1) it makes no sense to call Federer the greatest of all-time when one player completely dominates him on a particular surface and (2) Nadal also has a good head to head record against Federer on other surfaces: they are tied 6-6 on hard courts--with Nadal leading 6-2 on outdoor hardcourts--and Nadal also owns a Wimbledon win against Federer, proving that Nadal can beat Federer on Federer's absolute best surface even though Federer is almost completely helpless against Nadal on Nadal's best surface.
If this were just some small sample size fluke--if Nadal owned, say, a 3-0 record against Federer on clay but had never beaten Federer anywhere else or won any other Grand Slam titles--then it could be dismissed as insignificant in the context of Federer's entire career but the sample size is sufficiently large and Nadal's career is very impressive in its own right: Nadal owns a career Grand Slam just like Federer and Nadal has a better Grand Slam event winning percentage (.333 to .309) and a better Grand Slam match winning percentage (.877 to .869). Is Federer more durable than Nadal? Yes, unquestionably. Will Federer finish his career with more Grand Slam titles than Nadal? Probably--Federer leads 17-11 and could conceivably add to his total, making it very challenging for Nadal to catch him even if Nadal does not miss any more Grand Slams due to injury. Federer is tennis' Emmitt Smith; Smith is the NFL's all-time rushing leader but no serious football analyst considers Smith to be the greatest running back of all-time: Smith was great and he was very durable but his per game and per season rushing averages do not match up with Jim Brown's.
The greatest player of all-time discussion in tennis really must be split into at least two parts--Open Era and pre-Open Era--because if Rod Laver had been permitted to play in the Grand Slam tournaments throughout his prime before the Open Era then he likely would have set records that never would have been broken. The equipment, rules and playing surfaces have all changed so much over the years that it may be more difficult to make meaningful cross generational comparisons in tennis than in any other sport.
Setting aside any discussion of Laver and the other pre-Open Era greats, is Federer the greatest player of the Open Era? Is Nadal the greatest player of the Open Era? With all due respect to those two tremendous champions, the correct answer may be "Neither": a strong case can be made that Bjorn Borg is the greatest player of the Open Era. It is hard to pick Federer after he has been so thoroughly dominated for his whole career by his main rival and neither Federer nor Nadal have matched the winning percentages and the simultaneous grass court/clay court dominance that Borg established during his reign.
It is somewhat speculative to compare Borg to Federer and Nadal since Borg never competed against either player, but we have seen Federer and Nadal compete against each other many times--and, while it can be debated exactly where to rank each one on the Open Era list, it is increasingly hard to justify placing Federer ahead of Nadal: we have no video of anyone consistently beating Jim Brown and the only footage of Ruth, Jordan or Gretzky being outdueled comes from the tail end of their respective careers. Federer has been number one in the world as recently as October 2012 and he still maintains a number two or number three ranking depending on the week; Federer's fans trumpet his every tournament win as further "proof" of his greatest of all-time status so, by the same token, every crushing loss to Nadal further proves that said status should never have been granted by the media in the first place.