I’ve been taught that the most dramatic stories come from having protagonists who have to do what comes most difficult to them with a fervent desire to accomplish their goals, and lacking intelligence is one way to stack the deck against the main character. You want your hero to struggle, to earn his progress. Protagonists in manga, particularly shounen manga, are often designed to not be the sharpest tool around. Be it Naruto, Goku, or any number of heroes who act before they think (or omit the second part of that combo altogether), the reason why they’re made to be dumb is to make them more of an everyman, to tell its readers, “Hey, this could be you.” However, with some readers an opposite effect occurs, and you’ll often see people gravitate to the supporting characters on account of the heroes being, at least in their eyes, bland or possessing little merit as characters.
In trying to make the hero an everyman, authors run the potential risk of making their hero a no-man, someone to whom the reader simply cannot relate, but I don’t think that’s the problem at hand. I have this feeling that some readers do not wish to see certain negative traits in a story’s most important characters. Sometimes it’s because they’re passive, other times because they’re idiots, and other times because they are totally moe.
There’s a division of sorts when it comes to making this kind of shounen-esque protagonist. Should you have a protagonist that acts as a stand-in for the reader, to allow the reader to be immersed in the world, to feel as if he or she is the one saving the day? Or is it more important that the hero be someone who is already skilled, someone the reader can look up to? Both are paths for readers to live out their fantasies through protagonists, both are forms of wish-fulfillment, but each is different in the types of interaction required by the reader, and people may prioritize one over the other.
I have to wonder if age of the reader factors into this division of stand-in protagonist vs larger-than-life protagonist. The stand-in protagonist is something that I think appeals more to that crowd of boys 12 and under who run around in the school playground pretending they can fire lasers. Meanwhile, the larger-than-life protagonist seems to appeal more to the rebellious teenage crowd. A magazine like Shounen Jump has readers well beyond its originally intended audience of young boys, and disagreements as to what makes a good main character in a shounen series may simply be a result of different groups reading the same story.