Before we talk about Kabuto. Lets start with knowledge itself why it's so useful. Knowledge is useful information and can be use for any purpose. It has good explanation to problems people have. However, knowledge is not always perfect. Even if this was the case, added knowledge will have a better effect in the future. In order to seek out knowledge. Questions need to be asked and ideas thought. This will allow you to fix upcoming errors in the future.
Now this is what knowledge did the Kabuto. If a person believes that he has a justified, true belief then he has no reason to listen to criticism of his belief, or anyone else for that matter. Any idea which contradicts a true belief must be false. Therefore, all criticism is irrelevant, and anyone who disagrees is mistaken. The only thing to do is educate them, not debate with them, and not consider that they might be right and we might be able to mutually learn from each other. Confidence that one definitely knows the final truth leaves one with no reason to try to correct errors, it's actually foolish (Reminds me of NarutoBase)
Kabuto in a sense wanted to gather all the things in the world. Just like in the footsteps of Orochimaru, he wanted to become the perfect being and seek the hidden knowledge of jutsu of the world. And he was almost close the achieve perfection. But like I said. It was arrogance that blinded him of seeing what was wrong with himself. He did not trust himself and thought that by gathering the things in the world he can become someone that he's not and live by that. That's why Itachi was sure of his defeat.
Itachi has a keen insight to understand people. He can read emotions, thoughts, and movement easily. He has plan ahead on more then one occasion. Itachi does not need much time to figure out a certain weakness in someone. And he has the skill to overpower someone with his intel. He too had knowledge and used it for his benefit to protect Sasuke and his home. Itachi was a master of deception and intellect.
Now if it was me to choose who is the smartest I say Kabuto. However, Kabuto stand no chance with Itachi's intelligent persona. Kabuto in order to succeed in life, he has to believe in himself. Something he has not done in years. And maybe Izanami might teach him a few lessons. And it might change him for good or worse. So what do you think?