This is one of those threads where everyone has a point, and they all contradict merely on how one defines "better". One can see better in many ways.
1. One who wins the biggest prizes - Nadal has the edge here.
2. One who wins more often than not - Djoker has the edge here.
3. One who exhibits better tennis skills. Even this is a little subjective.
a. For some, tennis skills should be about shot making skills, excluding mentality and physicality the sport demands - Djoker has the edge here.
b. For some others, tennis skill is the whole package including mental and physical edge - Nadal has the lead here.
I'm one of those guys who defines "better" as in 2. and 3.a. Hence my vote goes to Djokovic. Nadal's better win% has significant clay bias. This is how their win% on different surfaces look like during their prime years:
Nadal, 2007-2014
Grass: 81%
Hard: 80%
Clay: 95%
Djokovic, 2008-2014
Grass: 83%
Hard: 85%
Clay: 82%
Djokovic leads on 2 of the 3 surfaces and has no weakness as much as Nadal on hard. I know I have counted a year more for Nadal than Djokovic, but you also have to keep in mind that Djoker often plays full season while Nadal succumbs to injury. Definitely the player who plays more should get the advantage here.
Nadal is unbelievable though. The mental aspect of the sport shouldn't be underrated. The guy has just 3 weapons - FH, legs, mentality. It's phenomenal what he has achieved with these.