Novak has Federer beat in pretty much every category now and he's positioned to take the slam race. It's really hard to argue Federer > Djokovic outside of being biased.
I understand the argument for having Federer at #2 given all his achievements, but when you factor in the H2H with Rafa it's just Nadal for me. Nadal also had to contend with both Federer and Novak's peaks for his entire career.
Now looking at Rafa, he has a much better H2H against Federer, beat him consistently during their respective primes, and is 10-4 against him in slams including a winning record at both the French and Australian Opens - 2/3 slams that they've played at. Not to mention that Nadal successfully dethroned Federer at his best slam whereas Roger failed to do the reverse over and over again, even suffering a humiliating 6-1, 6-3, 6-0 loss.