The only doubt I have with Djokovic is this feeling that a peak Federer would have taken him out, and I'm basing this on the very close matches between past it Federer and close to prime Djokovic at USO twice and Wimbledon twice. I think younger Federer beats him at his peak more often than not, but outside of peak, Djokovic dominates him. Considering that most players spend their career outside of their prime... Djokovic eventually comes out on top in any match-up.
Federer - Djokovic was always the most interesting match-up since they both like the same surfaces, hard, grass, indoors, with clay their weakest surface. So they can match-up on similar conditions. Nadal is the opposite, he likes clay the most by a mile, and there's not much more he can do on that surface that he hasn't already done. His domination at RG is something I can't see being broken. Can't think of another record in sport with lower chances of being broken than Nadal's no of Roland Garros wins.