Sasuke beating powerful shinobi does not make him more intelligent. Please take note that the thread is about who is smarter, not who is stronger. No doubt Sasuke is a great battle tactician, but he is also gifted with among the best jutsu due too his lineage and Orochimaru's training: Sharingan, very good reflexes, athleticism, Susano'o, Amaterasu. With those powerful abilities to assist him, it is waaaay easier to formulate tactics against opponents than Shikamaru who is basically a weakling. This makes Sasuke pretty much on par (if not better) in terms of speed, power and reflexes with people he has faced and defeated. When facing people stronger than him in the manga (i.e. Bee, Onoki), he was pretty much overwhelmed and was not able to come up with brilliant tactics to turn the tide.
Now let's take a look at Shikamaru. He is among the best strategist/tactician in the manga, but how good is he really in terms of being a shinobi? He only has the shadow manipulation techniques which have certain limitations and is not even a killer technique. Feat-wise, I would say he is pretty weak physically and his reflexes seem not too good. He appears to lack in speed, power, and reflexes which most Jounin have. He only has his intelligence but even so, he still managed to defeat Shinobi that are waaaay stronger than him. This speaks volumes about his intelligence, seeing that he does not have uber techniques and athleticism at his disposal. Now, say for instance Sasuke were to become as weak as Shikamaru (same power, speed, jutsu, and athleticism as Shikamaru), and was left to rely on his cunning and intelligence for the most part, I doubt he would have done as well as Shikamaru.
To make the long story short, I'd say Shikamaru is smarter.