Wow, you guys are really sucking up to Kimimaro.
Shikamaru can beat Akatsuki members because of his intelligence. Shikamaru can even analyze Madara.
Shikamaru would have Kimimaro's bone technique figured within a few seconds.
Shikamaru would win this. Especially if Gaara gave Kimimaro so much trouble. Plus, Kimimaro is a Part I character, Shikamaru is in Part II and even stronger.
I can see the scenario being... Kimimaro gets his bone dagger out. Shikamaru immediately hit him with his shadow technique. (Kimimaro is a close range fighter, which is to Shikamaru's benefit) Shikamaru makes a stabbing motion toward his own chest with a fist and Kimimaro follows in suit, stabbing himself in the heart. (Unable to block his heart as well at this point considering he's under Shikamaru's control)
And it's over.