Yes, but Federer's game works better across what variety of surfaces we still have. He has - or at his peak, had - one significant weakness on one surface that pretty much only one of his contemporaries was ever able to exploit. Nadal has more holes in his game on more surfaces that more players are able to exploit. He is a bit faster than Federer - although people underestimate how fleet of foot Fed was at his peak - and he is able to generate more topspin (although again, people underestimate how much spin Federer can generate), but as I said, in every other aspect of "talent", whether technical or athletic, he is inferior to Federer.
I disagree with you but I don't want to launch that other debate.
But in other periods of tennis, yes clearly Fed would have had more natural talents.
Anyway, even in today's period, Nadal still has his massive "Achille's heel" in his legs (and their adequation with his footwork).
And even if I also think that the H2H between Fed and Nadal is overrated and not representative at all on hardcourts.