First of all, it absolutely does matter that Nadal owns Federer H2H. However, we all know how Agassi operates. At the root of everything, is Agassi's insecurity, related to his jealousy of Sampras.
Sampras owned Agassi H2H in big matches, had more Majors, more weeks and years at #1 and was much more dominant at Wimbledon and the US Open.
Agassi played longer, won all 4 Majors and competed against a generation of players that Sampras didn't. It's very convenient for Agassi, after being beaten convincingly by Sampras in his last match in the final of the US Open, to claim that Federer and Nadal are at a different level than Sampras. Agassi is basically claiming that since he played against both generations of players, that the Federer/Nadal/Djokovic era is better. I suppose that is how he justifies the idea that Federer and Nadal are better than Sampras and Agassi is an expert because he played them all(except Djokovic). Sampras isn't an expert because he didn't compete with Federer and Nadal on a regular basis. I'm sure Agassi brought up the fact that Sampras lost to Fed at Wimbledon. Agassi is a jackass.