There are areas where shinobi are very intelligent at. You cant have one person as most intelligent wheres in other areas, he isn't intelligent at them. Eg, Shikaku and his son are intelligent in analysing and tactics, but they're not intelligent in manipulation, science or acknowledgeable in techniques and history.
This would be my perspective of intelligence:
Analysing:
-Kakashi Hatake
-Shikamaru Naara
-Minato Namikaze
-Itachi Uchiha
Science:
-Madara/Orochimaru
-Kabuto Yakushi
Tactics and Plans:
-Madara Uchiha
-Shikaku Naara
-Shikamaru Naara
Manipulation:
-Madara
-Obito
-Orochimaru
Knowledge on History and Jutsu:
-Madara
-Orochimaru
-Tobirama
Wise:
-Itachi Uchiha
-Hiruzen Sarutobi
-Tobirama Senju
-Hashirama Senju
The only way to know who is smartest is by looking at these perspectives and see who has the most scores in all of them. This would be mine:
1-Madara Uchiha: a cunning shinobi. He created the ultimate plan. He has tactics to even fight Juubito, and the whole alliance single handedly. He is master manipulator who brainwashed Kirigakure and Obito. His vast knowledge of history and techniques of shinobi. He is genius in understanding the human body and capable of creating humans by cells.
2-Tobirama Senju: a natural genius. He created some of the most powerful techniques of all time. Kage Bunshin, Edo Tensie and Flying Thunder God. It is he who most likely developed tactics against the Uchiha. He was able to analyse Obito's black orb right away. He is acknowledgeable of Yin Yang techniques. He was able to construct Konoha to what it is today by creating Chunnin exams, ranks of ninjas, schools etc.
3-Orochimaru: intelligent as a snake. He created so many forbidden jutsu. He is scientist and doctor when it comes to science as he created a dimension, studied Juugo's clan techniques, and capable of creating seal marks by using science. He was capable of making hypothesis by the Uchiha Tablets and discovered Madara's body secrets. He manipulated countless people even though most were children. He created tactic to fight against Konoha. He fooled Sunagakure.
4-Shikaku Naara/Shikamaru Naara: like father like son. Both are clever in creating tactics and strategies against an army of zombies. Capable of analysing and creating tactic of defeating the powerful Juubi.
5-Itachi Uchiha: as what he was hyped to be, an intelligent person. He analysed the weakness of a jutsu capable of creating the moon and created a tactic of beating it in seconds. A wise who uses words of elder people since the age of 7.
