In no particular order:
- Neji - Byakugan prodigy. Albeit he was from the branch family, he advanced so far with his Doujutsu based techniques.
- Sasuke - He's severelly under-rated on this site for no apparent reason, when he is one of the most intelligent individuals in the manga. Orochimaru commented that his intelligence was pitiful before Sasukes, Shikamaru looked up to him, and plenty of people vouched for his prowess. In fact, his battle strategies prove so.
He excels in several domains and is three of the only ninjas that have demonstrated so; the other two being Itachi and Kakashi.
- Kakashi - I may not like the guy, but I will never hold this it against him that he's an all-round extremely intelligent Ninja. Just like Sasuke, the guy is good at just about everything; from setting traps, to tailing, to ninjutsu. These are feats of an excellent shinobi and Kakashi demonstrates that.
- Itachi - A loathsome guy for me, but another insightful and cunning ninja like his brother and kakashi. He has demonstrated keen insight to develop counter strategies for just about any situation and hence is no different than the other two I posted.
- Orochimaru - He needs no validation in regards to creating a technique which lets you claim immorality. That alone trumps all his peers ever could have conceived of. He's head an shoulders above them.
- Kabuto - Like his Mentor, Kabuto has displayed shrewdness and intelligence to research and bring his data to a conclusive end. That alone speaks volumes for this young man who started off as a medic and mastered Dragon Sage Mode as well.
- Madara - Brilliant war-Lord who bested seasoned Senju war veterans when he was just a wee boy. His prowess in Uchiha-based Katon attacks is unmatched and his Kenjutsu skills rival Sasuke's easily. A cunning man with extra-ordinary combat and insightful skills. He deserves a spot here.
- Obito - Obito may not be your bright boy in a conventional sense, but man this guy is cunning. He is definitely a very fast leaner, which was profoundly evident how fast he grasped Uchiha based skills from Madara and became what he is today. He's fast, apt at using weaponry which is evident from is usage of Kusari-Gama - Sickle and chains combo - and his use of Ninjutsu is exceptional.
Not only that, the man kept all of his cunning and shrewd underlings in line and that alone is worth mentioning here.
- Tobirama - Another guy I have never taking a liking to, but he is definitely very intelligent, as he came up with Shadow Clones, Thunder God Technique, and Edo Tensai. All of these were used by the coming generation ninjas, and one of them was actually famous for this technique, when it wasn't even his own.
No one else. Shikamaru's so-called number and his feats do not match up at all. 200 IQ would make your head spin and yet, the aforementioned individuals have thought out battle-scenarios faster than he has and with better results on their own. His win against Hidan was laughable, given that the chances of that happening were close to none as he had no counter-strategies and no intel on Kakuzu, save for just one ability he saw to use threads and expands his limbs.
Honorable mentions would be Tsunade for being an exceptional Medic Ninja, and no one else.
