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Unlike Nadal, Federer hasn't lost to Djokovic on clay.... just saying.
You can make the argument that Novak should be in this spot over Federer. Ok, but would you say the same thing about Novak being number one over Nadal?
Why? Because Nadal has won five of the past six French Opens. That seems logical right? Of course. Nadal has demonstrated a consistent ability to win at the biggest and most famous clay court tournament in the world.
Well if Nadal weren't around, there is a strong likelihood that Federer would have a similar 38-1 record on the Parisian clay as Federer lost 4 straight times to Rafa—three in the finals and once in the semifinals—from 2005 to 2009.
Without Rafa, Federer is by far and away the world's best clay court player. And grass court player, and hard courts and carpet too...You get the point.
The way people are talking about Federer this year heading into Paris you'd think he wasn't even ranked. Yes 6-3 on clay isn't Federeresque but there are about 30 players who would take wins over Tsonga, Lopez, Soderling and Cilic any day.
Simply put, if Nadal is the best on clay, by that same logic Federer is an easy two.