You can't fault Fed for making a ton of finals on clay and losing to Nadal (the greatest clay court player ever IMO). Why does Fed almost always face other opponents in the finals of hard court tourneys? Nadal has never even made the finals of the US Open. The gap between Nadal and the rest of the field on hard courts is slim. The gap between Fed and the rest of the field on clay is still fairly significant. On a scale of 1-10, let's say Federer is a 10 on grass, a 9.5 on hard courts, and a 9 on clay. Let's say Nadal is a 10 on clay, 8.5 on grass, and 8 on hard courts. I'm not saying those numbers are accurate, I just pulled that out of my ass, but in theory you get the idea. Fed is a much more well rounded player on all surfaces. Yea he gets his ass kicked by Nadal on clay... but that's because he's constantly making the finals of clay tourneys even though it is his worst surface. Obviously their overall record is close on non-clay surfaces, but I agree with the sentiment that over a larger sample size Fed would prove more dominant. Let's see Nadal make the finals of a couple US Opens and I bet you Fed is waiting there on the other side of the bracket to kick his ass. Fed is definitely better overall, their head to head record means shit because Fed usually faces Nadal on clay. It's like if the Suns played the Lakers 21 times in a row in Phoenix. The Suns could easily go 13-8... something like that. Does that make the Suns the better team? No, just means that more often than not the Suns were playing with more favorable factors going their way.
But for the record, I do consider Nadal the 2nd best player of all time and I'm in love with his whiplash follow through on his forehand.