This is an excellent article. It exposes the flaw in the 13-7 H2H of Nadal vs. Federer and proposes that 29-20 STE (same tournaments entered) or 35-23 TTAT (titles in total fvailable tournaments) are what should really be looked at when comparing a "head to head" of Nadal vs. Federer. The author goes back to 2003 when using these.
I think that what really should be used, quite simple, is ranking. It is a long-term reliable measure, and really incorporates and accounts for everything. Or you could just use slams won out of slams entered, which also favors Federer, even since
Nadal won his first slam in 2004 (since Nadal won his first slam at the FO in 2004, Federer has won 13 slams, Nadal 6).
In response to those always arguing about the age differences, etc, I say, so what? Players don't peak at the same time; some come into their own very young, some later on. That would only be a reasonable argument if Nadal was a player like Federer, who you'd expect to have a very long career. Unless people think Nadal is going to get to 15 slams -- which I think is a real stretch, 11 is more reasonable -- that isn't a valid argument.
But even if you accept that, it is pretty difficult to say that a player isn't at or near his best after he has won his first slam.