Nadal, ranked No 2 in the world, has been dropped down to third seed for Wimbledon.
A unique formula created by the All England Club rewards players for their grass-court results over the last two years.
Federer typically plays the majority of grass events and has leapfrogged his rival to second seed.
That means Nadal could have to beat both Federer and Djokovic if he is to end his nine-year Wimbledon title drought.
The Spaniard criticised the British Grand Slam’s way of working by claiming it lacks respect.
But tennis legend John McEnroe is fully behind Federer benefitting from his past achievements.
“Well, it would be hard for him to really complain too much about Federer going ahead of him, considering what his record is at Wimbledon,” McEnroe told espn.co.uk
“But it could — it makes it where potentially he’d have to — he’d still potentially have to play two of them.
“Maybe if he was seeded two and Federer was on the other half, he’d only have to play one of them is what he’s thinking. So I get it, from both sides.”
Federer, Nadal and Djokovic are the heavy favourites to continue their dominance at Wimbledon next month.
But McEnroe would like to see some of the younger players break through.
“Now, the next generation, the younger guys like [Stefanos] Tsitsipas and [Felix Auger]-Aliassime, who are definitely I think going to win majors, and [Denis] Shapovalov has shown — he’s struggling now, but there’s some guys out there, and [Alexander] Zverev, there’s been a lot of pressure on him, and he hasn’t been able to handle it too well in the majors, but nonetheless, you can’t count these guys — they’re 22, 21, 20, even 18. They’re almost there,” he added.
“I think Tsitsipas beat Roger at Australia, but to get over there is a very tall order.
“If you look at Tsitsipas throughout the French, he had to play [Stan] Wawrinka, who he lost like a heartbreaker, 9-7 in the fifth, to play Federer, to play Nadal, to play presumably Djokovic or [Dominic] Thiem, that’s an incredibly difficult feat.
“This is one reason why they’re having their breakthroughs.
“You have to beat a couple of these guys usually in the same event. I would like to see it happen, personally.”
