Federer has not been at the level of these two players for a very long time.
Young tennis hopefuls, Thiem, Tsitsipas, Zverev but probably Medvedev and others, will soon take over the top of world tennis, Nadal and Djokovic are getting older and biology is working against them.
Still, I expect Nadal and Djokovic to dominate for at least another year or two because they are still psychologically stronger and better than young players.
Federer's injury I think has not really ever gone away at least from the way you see him play he does not seem to pull back as much as before but you are right,,, I think the Big 3 era is slowly Big 2, and hope to see even women's tennis get a big revival because Osaka is the hope from that side now Williams era is done with.
Experience can still win a little more but Tsitsipas I hope got a lot of lessons from this final:)