Both of them are good strategist, Lightning is a military and Nina manage the Mishima Zaibatsu. I think Lightning is probably better at coordinating, she shows more solidarity and regard for her partners and also can stand on them to prevent danger.
Nina is a freelancer, she prefers to work alone and can rely on her superior skills (mêlée, markmanship, firearms, stealth...) to carry out her mission.
After all, I think Nina would win because she can play tricky whereas Lightning is too honest. In a hand to hand fight, Nina has more skills, she doesn't have to worry about Lighning and would put the FF lady through hell.