Federer would have a big disadvantage. Clay courts are better for defensive play, because of the high bounces and what not, so its better to have clay on your side as you can chase more balls down. Grass is much better for offensive play, because of lower bounces, so its better for the other guy to be on grass. So Nadal can defend better as he is on clay and his balls will attack Fed much better as he is on grass. Fed will have to defend more, and his shots wont be as offensive because Nadal can just chase them down.
So: Nadal - ad. in
Fed - ad. out
This is all of course, if they don't switch sides.