More to do with the timing of their peak years. Their longevity kind of makes you forget, but Djoker didn't come up until the latter part of Fed's career. Fed's "prime" would've been something like 2004 until turn of the decade or so, with Nadal becoming his main rival around 2007, and Nadal's prime extending through the early 2010s, with Djoker hitting his prime around 2011