the intelligent one

There's the Punisher and Elektra. Although, their characters seem to be in the middle of superheroes and villains :) If you're speaking of intelligence, the most interesting character is the one who has beaten Superman -- Lex Luthor. No special powers, but has lots and lots of money (just like Batman). Batman wouldn't be Batman if he wasn't a millionaire.

In MArvel Universe Mr. Fantastic of Fantastic Four was considered to be the most intelligent person on earth. Even the smartest people in Marvel recognized his intillegence as beyond other people's mind.

I don't know many superheroes but I know 'Beast'/ Hank McCoy of Xmen is very intelligent. Beast possesses ape-like physical strength and agility and oversized hands and feet. After latent transformations to his physiology were activated, he has gained increasingly animalistic physical characteristics, extending to blue fur, feline facial features, pointed ears, fangs, and claws, and enhanced physical power and senses. Despite his savage appearance, he is a man of arts and letters and the sciences; he is a world authority on biochemistry and genetics, the X-Men’s medical doctor, and the Xavier Institute's (the X-Men's headquarters and school for young mutants) science and mathematics instructor. He is also a mutant political activist. Fighting his feral urges and fear of rejection, Beast dedicates his physical and mental gifts to the creation of a better world for man and mutant.