Intelligence is not a single entity.It cant be decided on one factor.
1) First thing, Shikaku or Shikamaru havent shown any "HIGH" Intelligence tactic yet,about shikamaru defeating hidan,just look how much time he took to plan & implement it..I'm not saying they're not intelligent,but they are good enough only for 'planning'.even Shikaku case,they already had intel about the enemy,so shikaku could prepare a best plan.They are not individually strong,but their strength lies in planning for a team/army. Shikamaru/shikaku wont be able to decide how naruto or any other individual will improve in battles,but they can plan out how a team of 5 ninjas can out match another 5. In short,they are able to 'plan' out a strategy,but they're not responsible for the implementation.
2) Second type is to foresee something well in advance & to prepare to counter it & battle tactics. first eg: Itachi, no need to write about him...he's too good in this thing....however,inspite of planning all this about sasuke, sasuke still chose the wrong path, so thats a failure too, but I'd say itachi had to take the risk of doing all this to sasuke. second eg: Tobi....many people doubt tobi's intelligence when they see him using chain against minato (especially in anime),however, they should also remember,he wasnt good in taijutsu, so he did all he could, & instead, see how he was able to infiltrate during kushina's pregnancy, he could enter the secret konoha barrier, seperate minato from kushina, take her away & extract kyubi....it's not that easy doing all that, & he had done too much planning..3rd eg: Minato.... about the tobi/kurama episode, as inspite of all the planning tobi did,minato was able to out-smart tobi(inspite of being unprepared), the way he hit tobi after ftg lvl 2, put a mark on tobi, did contract seal even before tobi could know....also, during his fight vs A, the way he put his mark on Bee & then landing perfectly to have a stalemate in order to allow his comrades escape...
In My opinion,most intelligent are:
a) when planning for oneself,
minato = itachi as no one can match their intelligence when it comes to tactics....they can figure out a strategy & more importantly, successfully implement it.
b) when given the resources & time, and planning for a team/army,
Shikaku = shikamaru, even though shikaku is more experienced, from what we've seen in manga,both seem to be equal.