The competition era holds no merit because :
1)After Nadal won his first slam, Federer and Nadal have won 13 slams each.
2)Federer has beaten more Grand Slam Champions of a slam at that slam en route to his wins. The count is 14-9 in Federer's favour. Moreover Federer has had to go through 2 GS Champions of a slam twice; Nadal has never had to go through more than 1 GS Champion of a slam(if that).
3)Since Nadal won his first slam in 2005, Federer has finished above Nadal in the YE rankings 6/10 times (2014 included). You can't cite injuries or pre-prime Nadal as an excuse here because a)We are choosing the year in which Nadal won his first slam and b)it also includes geriatric Federer. Besides 2 of the years Nadal finished on top of Fed were also Federer's worst years(depite the slam win in 2008) - the mono affected 2008 and his back injury affected 2013. He barely had any top 10 wins at all.
4)At the tournament where the competition is at its toughest and where exclusively the top players play, Nadal has never managed to win. Federer has done it a record 6 times.
5)A much more balanced slam count. Federer is miles ahead at 3 of the 4 slams (Nadal is light years ahead in 1 obviously). Showed that he could win the AO on both plexi and rebound ace.
We could get into all sorts of nit piking and factor in that Nadal won all but one of his non clay slams in the 2008-2010 period when Murray and Djokovic still hadn't peaked (and 2008 being Federer's mono period) etc etc. In the end it is what it is. Federer has virtually all the records and for now has a much better case for being the greatest of all time.
Ah, did I miss something? Yes, the H2H. Now, I don't think H2H is totally irrelevant. It is not - but there are a number of other criteria higher on the pecking order (in my mind, even consecutive SF, QF streaks hold more value). Also H2H is influenced by a number of factors viz :
a) Age - yes, Nadal is younger than Federer and prime Fed had a young Nadal who he *should* have beaten but 2004 Miami was unfortunate for Federer when he was sick and it all went downhill from there. There's no way he should have lost matches like 2006 Dubai. However, I think a younger player is always at an advantage (when the difference is 5 or more than 5 years especially) with regards to H2H. It is the reason why Federer went 9-3 against Agassi/Sampras combined.
b)Match up problem - this is something almost unique to sports like tennis. Match up makes a big difference. Have a look at Simon's Murray's and Berdych's records versus each other and you'll see what I am talking about.
c)Favoured surfaces - On Nadal's better surfaces versus Federer (slow hards and clay), they have met 25 times. The record there is 21-4 in favour of Nadal! On Federer's better surfaces/conditions vs Nadal(grass and indoors), they have met only 8 times and the record is 6-2 in favour of Federer. Do we penalise Federer for making it to more clay finals and reward Nadal for not making it to Fed in the latter part of the season. If Federer makes it past Djokovic in Zeus mode(being the only man to beat him in that form) to reach Nadal and loses there that is a slight on him, but if Nadal fails to get past Kygrios or Coric to meet Federer on his preferred surface, he gets a pass? Sorry, doesn't compute. I'd say the only two years where Nadal's and Federer's primes overlapped were 2009-2010 (I wouldn't begrudge a Nadal fan saying 2008 but he was so clearly struggling that year especially in the first half that I am not sure if I'd take that at face value in a serious H2H discusson). They met only once in that period in a slam - 2009 AO. That was a freaking close match. Consider this up until 2013, Nadal was leading on clay and Federer was leading on grass and hards!
Even accounting for all that I would definitely say Federer should have done more vs Nadal. It should have been at most 19-14 or thereabouts for Nadal even considering all the mitigating factors. It is definitely a blot on Federer's resume but not as much as is made out. The guy beat Sampras on Wimbledon as a teenager, Aggasi on hards in his early 20s(yes öld Agassi alongside who Federer won a slam in 2003 but if that doesn't count let's discount all of Federer's losses post 30), has bagelled Nadal on clay, hard and grass, bagelled Djokovic as a 31 year old on hards and at 33 is still the number 2 player in the world. The guy has game. Instead of mudslinging, let's appreciate the man. He could be gone in a year never to return.