Federer actually did pound Nadal's backhand to great effect in Indian Wells this year.
But historically, Federer's forehand hasn't troubled Nadal's backhand that much. Not because Nadal has a better backhand, but because Federer's forehand doesn't force errors the way Nadal's forehand does. Federer hits flatter and tries to hit around/through you. Nadal just wears Federer's backhand down with shots that jump to heights outside his comfort zone.
It's kind of like how Nadal's serve gives Federer so much trouble in comparison to Federer's serve vs. Nadal. It's just different styles causing different problems. I doubt anyone thinks Nadal has a better serve than Federer.
Nadal does and always has moved better than Federer, though. Nadal's recovery is unparalleled.