I agree with lots of your stuff, but not the last paragraph.
You can't really argue the fact that most of the titles Nadal/Novak won happened during the big 3 era, but most of the Roger's titles were prior to Nadal/Novak getting established? To me the level of competition increased a level when Nadal/Novak showed up, so that's why I put more weight on winning titles during that time. And this is before new crop of players came up. So now you could argue that any new slams that Novak wins will be on par with early Roger slams. Statistically, head to head, at their peaks or close to it, Nadal/Novak > Roger.
We talked about this before I think, and we'll keep continue to disagree