When Nadal has a three or four year period where he win's 3 slams a year, over 5 MS titles and WTF wins then I'll call him the best.
Until he wins another AO and Wimbledon, he will be second best.
Lets see what happens when we take away any of Roger's Slams
Wimbledon = 10 slams (AO 4, US 5, FO 1)
AO = 13 slams (US 5, Wimbledon 7, FO 1)
FO = 16 slams (US 5, Wimbledon 7, AO 4)
US = 12 slams (Wimbledon 7, AO 4, FO 1)
Lets see what happens when we do the same for Nadal
Wimbledon = 11 Slams (AO 1, FO 8, US 2)
AO = 12 slams (Wimbledon 2, FO 8, US 2)
FO = 5 slams (Wimbledon 2, AO 1, US 2)
US = 11 slams (Wimbledon 2, FO 8, AO 1)
When we compare the two player's best slams or most favoured, Nadal doesn't fare too well, with only 5 slams outside the FO since 2001 (13 years).
Federer on the other hand has managed to obtain 10 slams outside Wimbledon since 1998 (16 years).
Nadal has earned around 36 clay titles outside of slams. 63 - 36 = 27. 27 - 13 = 14. Nadal has won 14 titles not on clay
Federer has earned around 8 titles on clay not including FO. 78 - 17 = 61. 61 - 8 = 53. That's not too bad considering that's across two surfaces.
Regardless of H2H, it appears Fed has dealt better with the contenders of his prime meanwhile Nadal hasn't (outside of clay). Considering Nadal denied Fed numerous Masters on clay and slams it's a fair argument to say Fed has a better standing on clay since he generally lost to one person on that surface during his prime. Meanwhile Nadal (the GOAT) has lost to more players on surfaces outside clay.