I think that whether Nadal skipping the US open was a mistake or not will be decided by the outcome of this French Open final. Fully rested, not having to travel, quarantine and stuff, probably helped him a little, especially at his age.
Any of the 3 can be argued as the GOAT, depending on what angle you want to take. I have seen it said that Nadal had it hardest, because the first half of his career he had to face peak Federer, and in the second half peak Djokovic. But winning 'only' one AO is a problem, where Novak has been lethal. The narrative is that Federer had it comparatively easy, early on, but even when he'd win 2-3 slams a year routinely, he still had to beat Nadal in Wimbledon finals (06, 07), and defeat the likes of Safin and Roddick also. It's so even, that basically it's a case of pick your favourite.