The "era fallacy" is a great label and totally true.
You argue that Baghdatis, Gonzales, Roddick were not that good.
I argue that in 2011, Nadal was far from his best, Federer past his peak, and over players weren't factors. Thus, Djokovic profited of a sub-form from Nadal to beat him in 6 finals.
I argue as well that Nadal had no opposition on clay until his level drop last year, as he has only to face Federer, who I argue is a hard-court and grass specialist (I can argue that looking at his record), Djokovic, who was still progressing, and Ferrer, who is Ferrer. In fact, the best year of Nadal, 2010, happened just because their was no opposition anywere. Post AO, Fed lost his game as show his result in IW, Miami, RG, Wimby and US Open (he lost to an only incoming Djokovic). Djokovic too had a bad year, being ousted at RG by Melzer and Wimby by Berdych. Only at the end of the year he peaked. And of course, Soderling and Berdych, while they are no so bad, aren't really good either (just like Baghdatis, Fernando Gonzales and Andy Roddick).
Well, we can argue forever, there is no way to be sure. Thus, the era fallacy is a great theory.