In John Wyndham's The Chrysalids, one thing that might be considered a weakness in a society such as his is that he is adventurous and independent. In a civilization as intolerant as his, it is not terribly wise to approach anything in life lightly, especially in that everyone is watching everyone else. However, this could be excused by his innocence—he does not yet have an understanding of how dangerous things are for people who are different. He only gets a slight sense of this when he discovers that Sophie has six toes on her foot. The seriousness of his life is shown in that he does not know how to respond to Mrs. Wender's compliment:
"You're a good boy, David. You were very kind to Sophie. I want to thank you for that."
I felt awkward, and looked at my shoes. I couldn't remember anyone saying before that I was a good boy.
Mrs. Wender then tells David that he cannot tell anyone about Sophie's foot.
"It's very, very important," she insisted. "How can I explain to you?...If anyone were to find out they'd—they'd be terribly unkind to her."
David promises, resolved to say nothing to anyone, but he is puzzled. His lack of knowledge may be a weakness as well in that he is unable to know how to protect himself and others when the time comes. He will have to get over this quickly.
Then [the monotonous Sunday precepts join up] with a click that was almost audible..."and each leg shall be jointed twice and have one foot, and each foot five toes, and each toe shall end with a flat nail...And any creature that shall seem to be human, but is not formed thus is not human...It is a blasphemy against the true Image of God, and hateful in the sight of God."
Still David wonders how a little toe could be "hateful in the sight of God." He still does not understand the danger of this kind of intolerance. His naivete causes him difficulty when he casually wishes he had a third arm to help himself remove a splinter. Hearing this, his father beats him. This brings new understanding, as does learning that using telepathy to communicate is also abnormal.
David's uncle realizes the danger his nephew is in, even if David does not:
I want you to keep it a secret. I want you to promise that you will never, never, tell anyone else what you have just told me—never. It's very important: later on you'll understand better how important it is. You mustn't do anything that would even let anyone guess about it. Will you promise me that?
In truth, the only serious weakness I see in David is his innocence and inability to see the world for what it is. However, this changes over time. On the other hand, David is trustworthy, never telling Sophie's secret, fighting Allen to keep him from catching Sophie, leading the others out of Waknuk when they are discovered, and keeping Rosalind and Petra safe after they are captured in the Fringes.
I think the biggest weakness that we can point to in David's character is the way in which he is depicted as being a rather passive individual in a world where it is necessary to seize the initiative in order to survive. If you have a think about it, David, throughout the text, does very little that is active, and is reliant on others to act to save him from the desperate situation he and those with him find themselves in. In fact, the only instance I can come up with of David acting on his own initiative comes at the end of Chapter 14 when, having been ordered to leave the Fringes with Rosalind still there, he tries to double back to rescue her and is only captured easily and beaten up:
Just what they were expecting. But they didn't shoot me; they just beat me up and slung me back among the undergrowth. I remember flying through the air, but I don't remember landing...
Again and again, David depends on others or on luck to save him. It is Rosalind who is prepared and organised for when they have to leave Waknuk. It is his Uncle Axel who kills Anne's husband to save them all. It is Michael who assumes the leadership of the telepaths and keeps order. It is Sophie who releases Rosalind and Petra. David seems to be just a bystander in all of this frantic action, which is curious given that his father is such a strong man. Even when he does try to act, as shown in the example above, he is unsuccessful. Therefore David's greatest weakness is his passive nature and the way that he shows himself able to operate on his own initiative.