Well, we've talked about this before, but my sense is that Roger is tough as nails when he's ahead, but struggles more in close situations. In addition to the offense/defense matchup problem I mentioned above, this is the other major reason why he is below the other two in matchups. IMO.
This pattern of all three is reflected on the macro level of their careers. Roger emerged as the best of his generation in 2004 and utterly dominated them from that point on. Just a year before, in 2003, it looked like several guys were going to be equal, but Roger far surpassed them all. He coasted as the top player for four years. Rafa hung in there and pounced when he got his chance, and then had several surges when he reached the top. Novak was the third wheel behind the other two, seemingly always on the outside looking in for a good four years, and then finally put it all together in 2011.
Meaning, once Roger had not one but two guys of similar talent level--something he didn't experience in his early years--he had a hard time adjusting. He didn't have the early training that the other two did, in terms of being the third wheel. Early on he rose steadily and once he got to the top was able to maintain it, because he was just better than everyone else. I mean, one could argue that Safin, at least, and maybe Nalbandian, were close in talent, but they had other issues. But Rafa and Novak not only were incredibly tenacious, but both were defense-first players, and could neutralize Roger's offense. Roger stubbornly refused to adjust his game, because he had been imprinted with his early dominance. He finally figured it out with Rafa, although I'm still unclear how. With Novak, it feels like almost every match is close, which benefits Novak because he can wait Roger out until he blows it.