As already noted his stamina and mental strength were his greatest shortcomings. Those kill you against Nadal more than anyone else. Apart from those things and stroke wise and playing style wise he was a bad matchup for Nadal, and now that those things are rectified you really see it. Of course he is a better player than Nadal currently too, but Nadal is certainly right now a better player than an old Federer and Murray who both give Djokovic a harder time than Nadal, further indicating the truth.
As I said though, stamina, physicality, and mental strength are all parts of what make a player great. There's no such thing as, "Oh, he would be a great player if he had stamina/physicality/mental strength." That's no more valid than claiming, "well if Nadal had poor stamina, he would not be a great player." Well, the truth of the matter was that Nadal
does have great fitness, thus he isn't an average player and is in fact, one of the all time greats.
So to simplify the equation:
Pre-2011 Novak Djokovic had a stroke superiority advantage against Nadal. Nadal however made it up with much superior mental strength and stamina. Therefore, the net difference of Djokovic's stroke superior and Nadal's superior fitness had Nadal come out on top by a significant margin. 14-4 is complete, one-sided domination. Nadal won over 80% of their meetings!
Nowadays, Djokovic has completely turned the table. He was the one that matched Nadal stroke for stroke going on 6 hours, despite coming off a day's less rest, running more throughout the tournament, and coming off a bruising 5-setter against Murray. He was the one with more mental strength than Nadal.
So at the moment now, the net result is that Djokovic has better strokes than Nadal, better mental toughness, and just as much stamina. In fact, he was the one that outlasted Nadal at the US Open last year.
Also, the assertion that he beats Nadal easier than he beats Federer/Murray isn't entirely true either. He beat Murray by a bigger statistical margin than he beat Nadal in the AO. He also straight-setted Murray and Federer last year at the AO, and has
never straight-setted Nadal out of a grand slam.
So no, Federer and Murray don't always give Djokovic a harder time. They also can give him an easier time.
Djokovic first became a top player in late 2007. For the most part Nadal has been a much better player then Federer (the only exceptions being late 2007, and June-November 2009) since then, and harder for most everyone to beat.
Okay, let's take only the years where Federer was winning grand slams (2007-early 2010). Those were the years where Federer was still getting to every grand slam final, and the wheels hadn't come off yet. The stats also bear this out:
Roger Federer's record during that span:
2007: 63-7
2008: 66-15
2009: 61-12
early 2010: 10-1 (Federer had a bad spring after the AO, and didn't reach another slam final that year)
Cumulative record during this span: 200-35.
Winning percentage: 85.1%
Rafael Nadal's record during that span:
2007: 64-12
2008: 82-11
2009: 66-14
early 2010: 8-2
Cumulative record during this span: 220-39
Winning percentage: 84.9%
Nadal was better than Federer during most of this period, that's true, but the difference wasn't massive. But Federer supposedly has a matchup advantage, and Nadal supposedly has a matchup disadvantage. Nadal in this span raced out to a 14-4 advantage over Djokovic. Federer carried a 10-6 advantage over Djokovic in this same span.
How does this work? How does Djokovic carry a notably better record against the guy that supposedly holds a matchup advantage against him than the guy that he holds a better matchup against? Was the difference between Nadal and Federer so vast that it could overcome the fact that Djokovic had the worse matchup against the player he held the lower score against?
If so, the 'matchup advantage' and 'matchup disadvantage' that Djokovic has versus Nadal and Federer must not have been very vast or significant.
I, personally, think that the assertion that Nadal has lost because of a "bad matchup" to be pretty dismissive of what Djokovic has accomplished. Djokovic has been the better player for a year now. This isn't something new or inexplicable. When Djokovic is on his game, Nadal gets bossed on the baseline. The same is true against Federer and Murray. All of them have to change their game to play Djokovic.
NamRanger asserted that Nadal had to play more aggressive and go for shots he wasn't comfortable with against Djokovic, thus since he had change his game, this proves that Djokovic has a matchup advantage against him.
On the other hand, I said that Murray had to do the same thing. Ivan Lendl specifically told him to be more aggressive, to stand closer to the baseline, to go for more winners against Djokovic, which is decidedly not Murray's game. Does this mean that Djokovic has a matchup advantage against Murray too?
Is there anyone that Djokovic doesn't have a matchup advantage against, then?