Depends upon how you define "generation." 5-6 years is a lot in tennis time. It is the difference between a player cutting his teeth in Futures and entering his prime. Don't forget that Roger turned pro when Rafa was 12, Novak 11. I think of generation as having to do with player ages--who his peers are--while era has to do with the time. Generations overlap in eras, of course.
Or consider players within a year of them:
1980: Safin, Ferrero, Gonzalez
1981: Federer, Davydenko, Hewitt, Lopez
1982: Roddick, Nalbandian, Ferrer, Coria, Robredo
1985: Wawrinka, Tsonga, Berdych, Isner, Almagro
1986: Nadal, Gasquet, Monfils, Anderson
1987: Djokovic, Murray, Fognini, Querrey
1988: Del Potro, Cilic, Bautista Agut
There's a lot of overlap, obviously, but those are different generations of players, imo, overlapping in a broader era. Almost all of the players of Roger's cohort have long since retired.
Fun fact: Not only is Feliciano Lopez still playing, but Tommy Robredo is still holding on. He's lost in the 1st round of the qualifications of each three Slams this year.
I can see why you would group these as two generations, but I do rather agree with
@don_fabio above as to how much it matters. I also strongly disagree with
@Front242 above where he tries to insist that Roger is from a different "era" from Rafa and Novak. Clearly, that is not the case. See how many times they've played each other. They are all of this era.
When they turned pro and started winning tournaments does matter, in reference to your bolded above. Roger turned pro in 1998, at 16, one presumes (not yet 17, but maybe he was?) and won his first tournament (Milan, indoor carpet) in 2001, 3 years later. Rafa turned pro in 2001, at 15, just 3 years after Roger. So you make the point that Rafa was 12 when Roger turned pro, but it was only going to be 3 years until he did, too. And, at 12, he won all Spain and all Europe in his age group. And he also won his first tournament after 3 years, (Sopot, clay.) Novak turned pro in 2003. 5 years after Roger and 2 years after Rafa, and won his first tournaments also 3 years later (Metz, indoor HC; Amersfort, clay.) Roger and Rafa first played in early 2004, whereas Roger and Novak didn't first play until 2006. Nor did Novak play Nadal until 2006.
So I think you can see the complication of splitting Rafa and Novak from Roger, in some ways. By virtue of matches played, etc., Nadal and Djokovic have always been more like 2 years apart in "tennis years."
I think when they turned pro, and began winning does matter, and I mean for all players. For example, Wawrinka is a year older than Rafa, but turned pro a year after him. Always considered a "late-bloomer." And Isner, who is born the same year as Nadal, turned pro in 2007 (he played college tennis,) which is a full 6 years after Nadal, and you consider 5-6 years to be a generation, so does that make Isner and Nadal even of the same "generation?"
What I'm saying is that birth years don't matter quite as much as you make them, and you can put in that break, if you like, but there still is a bit of flabby in there. I do think tennis years matter. But we're also only talking about the start, and not the longevity of strong playing years.