As far as the dominance of the Big 3, let's take two statements:
1. The Big 3 dominated because the competition was weak
2. The competition was weak because the Big 3 were so dominant
We can focus on one side (the greatness of the Big 3) or the other (the weakness of the Big 3), or we can take a third--and, in my opinion, more nuanced--perspective: that it is a chicken-and-egg thing, and the two are not separable.
Let's take Roger, for instance. His detractors will say he only won 17 Slams because his generation was weak. His supporters will say his generation was weak because he was so great. We can imagine a scenario where Roger became a Swiss watchmaker instead of a tennis player, and certainly we'd see several players Hell, we'd probably see several players with more Slams--maybe Andy Roddick would be in the 3-4 category, maybe David Nalbandian would have a Slam or two. Andy Murray with 5-8 Slam titles. Now certainly there are no players in his generation who would have been all-time greats without his presence (true greats find a way to win, no matter the competition), but there are several excellent players who would have had better careers: Roddick, Safin, Nalbandian, Hewitt, maybe one or two others.
But we cannot know which is more causal: Roger being great or his generation being weak. All we do know is that Roger was extremely dominant over his generation and became a peer of the next generation of greats (not unlike Jimmy Connors or Ivan Lendl, actually, but more so).
As for cross-generational comparisons, all we can really do is compare players relative to their own generation. We cannot ask, "Who would have won, Rafa vs. Bjorn?" Actually, we can answer that easily: Rafa would have destroyed Borg. But that's taking things out of context. We cannot know what sort of player Bjorn would have been today, with modern training and equipment. It is a pointless speculation, in my opinion. But we can look at how great Bjorn was relative to his era vs. how great Rafa was relative to his.
One final thing. I disagree completely re: Rafa. When he came on the scene there WERE some very good clay court specialists among them Guillermo Coria, whose career and confidence (including service yips)--some believed--was greatly damaged by the emergence of Nadal. And don't forget that he dominated Roger on clay and Roger was an excellent clay player in his prime. He also holds the edge against Novak on clay, 14-7, although Novak his 7-5 on clay from 2011 to the present.
But do you really think that Rafa wouldn't have been able to dismantle Kuerten or Bruguera or Courier, or even peak Agassi? He would have dominated. Whether you like it or not, he is the greatest clay court player in tennis history.