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Jyu Oh Sei might work. Main is smart, and has to grow strong, too. Adversaries count on strength.
Tengen Toppa Gurren Lagaan might count. The hero is smart, but also strong (not from outset, gotta let it develop some epis). The villains are strong but also a bit smart (one guy at least).
Utawarerumono I think. Though the hero turns out to be not only smart towards the end at least
Evangelion might count. The lead is not stupid, is backed up by some super smart peeps, and the villain is strong indeed. Well, the obvious villain. The other guy (not sure whether to count him good or bad, though he is on the good side. Or is he?) is smart too. Lead is a bit wimpy though hm, not really the hero type.
I dont know whether important, but kinda side chars count. If so, Madlax might work. Some on the good side are quite smart to very smart. Heroine is smart and strong. But the villains are smart too, but rely alot on strength, IIRC.
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