Regarding the clay issue, yes that skews things and works to Nadal's advantage. But Roger beat Nadal on clay a couple of times and certainly had his chances in some of their matches.
So let's take out the clay regarding their major match up.
2-1 to Roger on grass.
2-0 to Nadal on hard/slow blue clay
No US Open I know. Nadal did not make the final because he is not great on the US Open surface bar that year he won the title, the year Roger did not make the final, and the year after when Rafa was the runer-up, when Roger also failed to make the final. So, they are both as guilty of ducking out of the finals.
All I am saying really is that in the matches they have played, not the matches we imagine, Nadal seems to play the better tennis because he, erm, wins. And in some people's eyes that makes Nadal the better player.
But I think the real problem is this.
We need two sentences for this conundrum to satisfy both camps.
1) Roger is the better player when it comes to overall abilty, style, his place in history
2)Nadal is the better player in the matches they have played against each other.
Somewhere I am sure there is a mathematician who could write a beautiful equation to express this.