Djokovic is much better from the back of the court and better off the return than Federer, and those are the areas that matter in today's game. If we had faster surfaces where having a complete game mattered, then Federer would be better, but all of Federer's tools are just 'nice things to have' while Djokovic has better 'tools that actually matter.' Federer may have a stronger serve/forehand, but they are not miles ahead of Djokovic's forehand/serve, and Djokovic by far has the much stronger backhand/return game, areas that are above average on a good day for Federer.
Essentially, Federer has stronger strengths, but Djokovic is a much more complete 'modern' player, as he literally has no weakness to exploit when he is on. Federer on the other hand, can be exploited even when he's on top of his game, especially since his game is basically incompatible with today's surfaces.
For all of Djokovic's alleged superiority in terms of being more well-rounded, it hasn't shown in the Majors except for in 2011, where, oh, he only showed parity with Federer at best. In no year has Djokovic demonstrated superiority to Federer's prime.
Other than against Nadal on clay, Federer's backhand wasn't exploitable in his prime, and ultimately he just wasn't exploitable overall, as his incredible W-L records demonstrate. Djokovic's W-L record suggests far more exploitability. And in Federer's prime, his return game was more than merely "above average" on a good day; he has a very good return game.
And for all of Djokovic's alleged backhand superiority, what good has it done him at the French Open? Stopped by Federer in 2011, his best year on clay, and unable to defeat Nadal at the FO on clay since. If he keeps up his level, sure, he'll probably eventually win the FO, perhaps beating Nadal in doing so; seems rather likely, but not because of any claycourt superiority, merely for encountering an older Nadal who's lost a step.
Djokovic is a great player no doubt, but if he were a better player than Federer, he'd be on pace to eclipse 17 Majors by now. That said, I expect him to get double-digits.
PS: Also, this "when on" proviso is key. Except for 2011, Djokovic hasn't demonstrated consistent utter domination like Federer did. He seems to blow hot and cold quite a bit. That is definitely a weakness for a player to have.