All I can say personally on this recent debate is:
Comparing achievements is simple. You have the numbers that cannot be changed at will.
Comparing peaks is usually subjective. Most of the time, a person leans towards his favorite.
However, it becomes completely pointless when comparing peaks that are several years apart. The matches we have at our disposal are not strong evidence. If player A who was not at his peak lost in a tight match or won against player B who was at his peak, it doesn't mean that player A will definitely beat player B in a peak-to-peak battle.
Look at some of H2Hs between Novak and Fed. In 2009, Fed's prime year, Novak had a 3-2 H2H. In 2014, Novak's prime year, Fed had a 3-2 H2H. So there is absolutely no rule that either would surely win a peak-to-peak battle.
Also, I see no reason to argue about level of play, would 2004 Fed beat 2011 Djokovic at USO or any other hypothetical. Federer fans have the right to think he at his peak would crush peak Djokovic at USO and Wimbledon. However if I were in their place, I would much rather be happy because of 5 USOs and 7 Wimbledons than trying to give bonus points/titles to him or downgrade another fantastic USO and Wimbledon player because of my own subjective opinion about peaks.
As a Djokovic fan, I couldn't care less what Federer fans think about Djokovic and how many greats they think have shown a higher level on certain surfaces than him. His 2 US Opens and 3 Wimbledons are however proof that he is a fantastic HC and grass player and that he would be a tough opponent for anyone. No win is guaranteed, but a good fight though is.