Stewart's allegory
Stewart's story is the story of lonely genius. As an exceptionally perceptive person, Stewart understands his rejection with more accuracy than others might, and although that means each event of rejection is extra humiliating, it also means that he can take refuge in the truth that, actually, we're all in this together, no matter what those people believe. However, the allegory is not just about peace. It's about growth too. Stewart's story is a challenge to the reader to be more social and more vulnerable.
Ashley's allegory
As an allegory, Ashley's story begins to take on the following meaning: "It's important to remember that people deserve a chance, because everyone is going through something difficult." For her, We Are All Made is a story of how she was challenged to have empathy for a weirdo, so much so that she begins to feel he is part of her family.
The twin unions
The parents' burgeoning romance is paralleled by the difficult sibling relationship that is growing between their children. Both couples are suffering from loss; Ashley and her mom are confused by the recent news that Ashley's father is gay. Stewart and his father are reeling from the death of the mother, and yet, the adults know that being alone is not an option. Their union literally forces their children to make friends in unlikely places.
The science motif
Part of Stewart's fascination with science seems to be that he can draw connections between scientific fact and his own conscious experience of life. For instance, several times, he educates his new sister about some interesting science fact that has direct parallel to her life. He brings knowledge into a new light for her, spurring her on toward her independence.
The question of death
Death is symbolized in two ways. For both children, death occurs to a parent. For Stewart, it's the literal death of his beloved mother. For Ashley, it's the death of the life she expected for herself and her parents. It's the death of their marriage, and the it's also the death of her naivete. She is forced to face these things with a higher maturity than she has ever been forced to demonstrate.
