Itachi was said to be the greatest student the academy had ever known since it's foundation, this alone should say a lot.
忍者学校(アカデミー)
始まって以来の天才・・・
あの子ほど優秀な生徒は今までいませんでしたよ
He(Itachi) was the greatest genius the Academy had seen since it's foundation.... There hasn't been a finer student than him.
Also being an anbu captain at 13 years old should speak volume of his intellectual abilities as well as offensive power. I dont think it was implied that Itachi was leading Kakashi, as i believe Kakashi was a captain himself, but the difference lies in what Kakashi pointed out ;
The fact that Itachi was captain at 13 years old. Anbus are ur highest ranked ninjas tied with Jounins (Shikaku, Kakashi, Asuma). Itachi was leading these guys when he was still a child, leading people is not about offensive power, it's about leading a team. As shown with Shikamaru, it didnt matter if he was strong or not, he was assigned leader because he had the brain to do so. Itachi was leading the greatest out there and given Kakashi's reaction, i doubt he himself was a captain at such a young age. It had to be a hell of a feat to pull someting like this.
Itachi, Minato, Shikaku, Kakashi and Shikamaru are without a doubt the smartest of the serie, and the gap in their intellectual abilies is extremely small but i still think that the best Kakashi can hope to achieve is to equal Itachi. Itachi is without a doubt the wisest shinobi in Naruto, and because of this im also bound to believe that he is the smartest overall, specially with the praise he was given by the academy as well as the fact that he was captain of the anbu at 13.
And as it was pointed out before, Kakashi had 4.5/5 in Intellect in the first databook which is when he was 26 years olds and experienced. Itachi at 21 was already at 5/5 and there is no telling if that stat had just recently capped.