Also, I think one of the reasons why people rate Nadal higher than Djokovic is the surroundings of his ascent. Nadal wrestled the dominance of tennis away from the greatest player of all time. He beat him in his backyard in 5 sets in probably the best tennis match ever. He won all 4 GS titles before Federer and Djokovic. He had the biggest opponent possible and he overcame him. Djokovic on the other hand didn't dominate until 2015 and 2016 - when Nadal was injured most of the time, Federer had injuries and his problems with ageing, Murray was injured a lot around that time too. That also explains the huge difference in the #1 stats.
Djokovic just didn't have to wrestle it away from an all-time great like Nadal.
Yeah, you're right, Djokovic had to wrestle it away from 2 all time greats, not just one. Nadal had won the last 3 slams of 2010, Federer had won the Australian open and lost to the eventual losing finalists in 2 quarters, and one semi, of the other slams.
Then Novak Djokovic came out with a 41 match, 7 tournament win streak to start the season, beating Fed en route to victory in Australia, and losing only to one of Federer's greatest performances at Roland Garros. He then went straight to Wimbledon and won (beating Nadal in the final - his play in the first two sets was scary), won another two tournaments, retired from a 3rd in the final with injury, then went to the US Open and beat Roger in the semi and then Rafa in the final. Injuries then set in and he lost another 3 games but the guy had a 70-6 year regardless, in the era of Roger and Rafa at their peaks.
The next year he beat Rafa in a 5h 53 Aussie Open final, before reaching the Roland Garros final on the verge of holding all four slams at once; something neither Roger nor Rafa have done, then or since. He was actually turning the match around in his favour before a rain delay allowed Rafa to recharge and come back the next day to finish it in 4 sets. That Federer won the following Wimbledon is only evidence that at 30, Federer wasn't far off the all conquering dominant Roger of 3-4 years prior.
So no, Djokovic was already dominant in 2011-12, winning 4 of 5 slams, beating Roger on the way to 2 of them and Rafa in 3 of the finals. It was at this stage, already, that Agassi and McEnroe had him up there with the all time greats, with Rafa calling it the greatest season he'd ever seen (bear in mind that Rafa played through those 4 successive seasons of 3,2,3,3 slams from Roger). And he did all this with Roger just off peak, and Rafa in his absolute prime. There's a strong argument to say that Federer probably still was at peak then, he was just getting beaten by better players.