Kakashi's smart through his experience as a shinobi and his natural genius skills as a shinobi. Shikamaru is intelectually smarter then Kakashi due to his IQ. Kakashi is a strong strategist but Shika has him there. Kakashi's experience however gives him an edge for he is able to think beyond the mere statistics, and the layout of a battle plan (like in a game of chess).
Kakashi is smarter in experience
Shikamaru is smarter intellectually (although Kakashi is a good match for him in this catagory as well)