Charles Wallace looks like a five-year-old boy, but he talks like a professor and thinks like a psychic and a physicist rolled into one. He reads his sister Meg and his mother like a not-very-difficult book, even though he can't actually read books yet:
"It's being able to understand a sort of language, like sometimes if I concentrate very hard I can understand the wind talking with the trees. You tell me, you see, sort of inad– inadvertently. That's a good word, isn't it? I got Mother to look it up in the dictionary for me this morning. I really must learn to read except I'm afraid it will make it awfully hard for me in school next year if I already know things. I think it will be better if people go on thinking I'm not very bright. They won't hate me quite so much." (2.81)
Charles Wallace breaks the genius stereotype in that he doesn't just have book smarts, he has people smarts too. He knows that being seen as a genius sets a kid up to be the class punching bag, and that putting on a mask of stupidity is sometimes safer. While Meg wants to do things (like math) her way or not at all, Charles seems ready to do what he can to keep a low profile.
Charles Wallace's differences from the norm go beyond his intelligence, though. His mother suggests to Meg that he's practically a new species of being:
"Charles Wallace understands more than the rest of us, doesn't he?"
"I suppose because he's – well, because he's different, Meg. […] Charles Wallace is what he is. Different. New."
"But Charles Wallace doesn't look different from anybody else."
"No, Meg, but people are more than just the way they look. Charles Wallace's difference isn't physical. It's in essence." (3.87-100)
Mrs. Murry's use of the word "new" suggests that, in her mind at least, Charles Wallace is more than your run-of-the-mill boy genius. It's unclear whether she knows more than she's telling Meg about how, exactly, her youngest son is Human 2.0, but Charles Wallace's uncanny knowledge and apparent superhuman powers elsewhere in the book suggest that she's on to something. And by keeping the exact nature of Charles Wallace's difference vague, the book avoids the coming up with a pseudo-scientific explanation that trespasses into goofy land.
Being the smartest kid on the block (and possibly the planet), Charles Wallace has unsurprisingly developed a pretty high opinion of his own abilities. Pride goes before a fall, however, and Mrs. Whatsit warns Charles to watch his step:
Mrs. Whatsit looked at Charles Wallace, and the creaky voice seemed somehow both to soften and to deepen at the same time. "Charles Wallace, the danger here is greatest for you."
"Because of what you are. Just exactly because of what you are you will be by far the most vulnerable. You must stay with Meg and Calvin. You must not go off on your own. Beware of pride and arrogance, Charles, for they may betray you." (6.92-95)
Warning Charles Wallace not to think he's all that is kind of like warning Timmy not to fall down the well or warning Bella not to fall in love with Edward – saying it makes it more, not less, likely to happen, by the law of narrative foreshadowing if nothing else. It's interesting that Mrs. Whatsit specifically warns Charles Wallace to stay with Meg and Calvin: the antidote to Charles Wallace's pride is not just being aware of his own liabilities, but also maintaining a strong connection with others. And since the kids are about to go up against a giant brain that gives even Charles Wallace a run for his money in the smarts department, the emphasis on human connection over sheer intelligence looks forward to the conflict that is to come.
Of course, once Charles Wallace faces off with the man with the red eyes, all Mrs. Whatsit's advice goes out the window.
"Try to find out who I am, then," the thought probed. […] "Look into my eyes. Look deep within them and I will tell you."
Charles Wallace looked quickly at Meg and Calvin, then said, as though to himself, "I have to," and focused his clear blue eyes on the red ones of the man in the chair. Meg looked not at the man but at her brother. After a moment it seemed that his eyes were no longer focusing. The pupils grew smaller and smaller, as though he were looking into an intensely bright light, until they seemed to close entirely, until his eyes were nothing but an opaque blue. He slipped his hands out of Meg's and Calvin's and started walking slowly toward the man on the chair. (7.104-107)
It seems that Charles Wallace's tragic flaw here is not just his confidence in his own abilities and that he will able to pull back when he needs to, but also his desire to know at all costs. This harkens back to Meg's uneasiness at not understanding things (such as Charles Wallace himself, for one), followed by her eventual acceptance that there are some things she'll just never understand, and that's OK. While the stakes may be higher here, since what Charles Wallace wants to know is who this guy is and what he's done with Charles's father, the fundamental dilemma is still the same: is the quest for knowledge worth its costs? When is it better to just accept one's ignorance and move on?
When Charles Wallace submits to the man with the red eyes, he becomes a pale replica of himself.
Charles Wallace sat there tucking away turkey and dressing, as though it were the most delicious thing he had ever tasted. He was dressed like Charles Wallace; he looked like Charles Wallace; he had the same sandy brown hair, the same face that had not yet lost its baby roundness. Only the eyes were different, for the black was still swallowed up in blue. But it was far more than this that made Meg feel that Charles Wallace was gone, that the little boy in his place was only a copy of Charles Wallace, only a doll. (8.1)
This fake Charles is creepy as only lifelike dolls and CGI humans can be. And while Chucky has little in common with the real Charles Wallace besides his face, he does fulfill his namesake's most fervent desire: he takes Meg and Calvin to where Mr. Murry is imprisoned. Would the kids have been able to be reunited with their father if Charles Wallace hadn't gone over to the dark side? Was Charles Wallace's decision to let himself be taken over by IT actually the best one under the circumstances? It's hard to say. But by setting up the conclusion so Meg has to save her boy genius brother through the power of love, the novel suggests that brains aren't worth much without a heart.