Nadal dominates in only particular clay conditions, and Madrid hasn't ever really suited him.
And even if the conditions were ideal for him there, Djokovic looked perfect in the MC final and Nadal's form was sub-par by his standards. Djokovic's top game this year > Nadal's top game this year, even on clay.
IMO, Djokovic A's game > Nadal's A game on clay (only since 2011). 2008 Nadal obviously has the highest peak on clay. However, Nadal's B game will always be >>> Djokovic's B game (on clay). That's why Djokovic can't beat Nadal on clay unless he plays with his A game (for most of the match at least).