For a dude who I regard as one of the most sensible on this site sometimes you show you also have biases like we all do.
And that's ok.
You are also human.
*takes troll mask off*
Here’s what I actually think: the two are close enough in ability that I think most matches between them at their peak would be close, but obviously it depends on the tournament since they’re better in different conditions. All the big tournaments:
AO: Djokovic wins this, moderate margin. The one thing that makes me pause here is Fed’s 2007 run which stands up with some of Djokovic’s best matches at the AO.
IW: Federer, slight margin
Miami: Djokovic, heavy margin
Monte-Carlo: Djokovic, moderate margin
Madrid/Hamburg: It depends on if we choose to equate Madrid with Hamburg (the Masters it replaced on the calendar). Fed was excellent at Hamburg, better than Djokovic has been at Madrid, so I’d take him here if we did that. If not, Djokovic.
Rome: Djokovic, slight margin. This would be a much bigger margin if Rome 2006 didn’t exist.
RG: Gonna say 50/50, slight edge to Fed. Djokovic has been better at the tournament in the long run, but we’re talking prime vs prime here. Fed had some great performances in 2009 and 2011 that can stand up to Djokovic’s best matches in 2013, 2015, and 2016. Djokovic matches up better against Nadal but between the two I might go Fed slightly.
Wimbledon: Fed, moderate margin. I really don’t think prime Djokovic ever came that close to prime Fed on grass. Fed’s game at his peak was just perfectly built for the post-2000 surface.
Canada: Djokovic, moderate margin
Cincinnati: Fed, heavy margin
U.S. Open: Fed, moderate margin. Djokovic has had a number of great performances here, but he’s had struggles with form at some point in almost all of his runs, even the very best one in 2011 (he had an injury in the final and didn’t serve well). Fed on the other hand consistently delivered the goods in his prime. You can poke holes at 2005 and 2007 maybe but 2004 and 2006 were pretty much perfect displays (outside of the wind in the Agassi QF)
Shanghai: Djokovic, moderate margin
Paris: Djokovic, heavy margin. Fed has never been that good here. I mean he was good, but he never really delivered the kinds of masterclasses Djokovic was known to have in his prime.
YEC: Fed, slight margin. Again, Djokovic had great results at this tournament, but so many of Fed’s very finest matches happened here.
So basically I think Djokovic mostly outdoes Fed in the Masters and the AO, but Fed can just bank on a big advantage at Wimbledon and the U.S. Open. RG is pretty much a tie in their primes.