how i define intelligence was simple base on fighting tactics and how to deal with drastic measures including how to escape from them when in battle and when lost some one.....i would say shikamaru is one for the anime shown him as the potential smart ninga so it is simple why a lot of persons would select him....
As for me he is not because minato as such analytic skill are he has accomplish a lot at a young age including developing techniques of his own.....but when you look at how shikamaru from the naruto days not shippuden you could see his leader ship skills when ...ninga's using earth style had nearly kill he, his team and neji...he was even as smart to know that other ninga's was way a head of him but did not sweat only concern with what strategy he could use to accomplish victory..the hidan death was epic..with the little intel he got on him.....but remember the trunin exam with orochimaru subordinates that had cast genjustu on him on how quick he got out of it...compare to sasuke..who had sweat and had to grab a hold of his self when orochimaru him self had cast the justu...more to come
kabuto is smart but lack the capability to use is smartness to win battle...for me after shikamaru....and minato...itachi would be next seeing how he did kakashi who is forth..on the line up why kakashi 4th for pain said it him self ninga's like him should perish...i know you would want me to include jiraiya knowing he took down three pains an also allow itachi and kisami to flee but dat doesn't still took away the fact as a s class ninga he should have not got pass the barrier and got notice i also compare their level in class which relates their ability with their foolish mistakes...kakashi was also praise for his analytic skill by almost every ninga...the best would be trying to copy itachi ms....and predicting kakuzu iron technique
Why i choose some like deidara....he is an underated analyse seeing how he had took out gara was epic....so good i wish kishi plan more deaths like that....nagato..would be fifth but you would argue about manipulation by tobi but you have to look at it this way...tobi taught nagato was invincible being invincible you must have a great amount of intelligence in addition to how young he was...nagato words are absolute...when he speaks its hard to debate on what he says even is theory to peace was almost a 100% his meaning to for justice which he express was so good i almost taught it was actually correct....but u have think logical we have young children watching this....i wont go after 5th the rest you can build the order...tho in my words tobi then kakuzu