Yeah but you could argue the early meetings were Federer in his prime and Novak nowhere near ready to beat him.
Their last two meetings have been classics and Federer will be disappointed he’s lost them both.
Nadal was the only one who could consistently challenge and beat prime Federer (04-07). Novak wasn't a factor at that time, and Fed did beat him the 2 matches they had met (AO SF and US final of 2007).
For people who think I'm being selective about marking a prime, you can look up his win percentages by year. Year-long percentages will be less influenced by things like the form of rivals, etc, since they are mostly determined by winning the smaller matches consistently. He dropped off big-time in 2008, not just to Nadal but generally. And while he had a few bright spots after that (2009, 2012), none are comparable to peak 04-07... till we get to 2017 (92%), a year when Djokovic was again a non-factor.
Win percentages: 04-07
93/95/95/88
81% in 2008, a sharp fall.
(For reference, Nadal in 2007 was 8-6 vs Federer: 6-1 on clay, 0-2 on grass, 2-1 on outdoor hard, 0-2 on indoor grass.
At the same moment Federer was 5-1 vs Nole, 3-1 on hard outdoor and 1-0 each on indoor and clay.
Since then, Nadal pulled away a lot (23-10) before Fed caught up a bit (24-16). Djokovic matched him in 2015 and hasn't lost since.)