AsahinaInu
For instance, I mean I wouldn't consider Maes Hughes from FMA to be the smartest anime character that exists from some purely "look at the character sheet for his Intelligence score" standpoint, but the guy is written is such a way that you believe the intelligence that the guy does have is genuine as the author does a good job of showing you that the guy is intelligent, rather than just trying to tell you he's intelligent. Whether those types of characters are smarter or not than characters of intelligence beyond human comprehension, I still am more likely to go "Whoa! That guys got some brainpower." when presented with someone whos intelligence is shown to me.
You make a fair point about Hughes. Heck, a lot of characters from FMA are smart in their own way. Military soldiers, such as Roy and co. have high or decent amount of intelligence, and none of it is thrown at your face in the fashion of "Oh my god, this guy is amazing!". The Alchemists in general are also smart since they need to have a nice brain in order to use said Alchemy. And if we look at the old "smart means you know a lot", then Sheska would be more than qualified. The girl is a living library.
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