Rescuing the mother
There is an allegorical layer to the story since Bee is growing up. In her psychological growth toward adult independence, she must journey within herself to find her mother within. This is a commonly used literary technique, and it's a famous part of the "Hero's Journey." Essentially, the literal story is also a depiction of Bee's personal growth.
The architect
Architecture is a telling job for Bee's mother, because it speaks to two skills that her mother has in spades: creativity, and discipline. Bernadette is creative (a MacArthur "Genius" in fact), but we know from the technical demands of architecture that Bernadette is also an extremely hard worker, and a disciplined person, since building a luxury home is different than writing a novel or painting a picture, because it takes hundreds of people, and it takes serious engineering and mathematics. In order for Bee to follow her mother's example, she will need to keep her free spirit and develop discipline.
The Microsoft man
Elgin works at Microsoft, signifying his attachment to commerce and business. When he falls in love at work, it's a sign that he doesn't connect well with Bernadette, and it's his secretary whom he falls in love with, so perhaps what he doesn't like about Bernadette is that she doesn't submit to him the way he secretary does. In other words, Elgin represents a more traditional male gender role, and Bernadette represents the feminist rejection of those traditions. She just gets up and moves to Antarctica—that's how uninterested she is in being Elgin's pet housewife.
The unplanned pregnancy
For Bee and Elgin both, Soo-Lin's baby is a bit of a complication. First of all, Elgin wants to be with Soo-Lin, and when he finds out she is pregnant with his baby, he buys her a house (a sign that he will stay with her). Bernadette and Bee are like his "old" family now, and this baby represents the inevitable downfall of Bee's family. But, that's not necessarily a bad thing in this novel, because Bernadette felt enslaved to a boring life, and Elgin genuinely prefers Soo-Lin's company to that of his wife.
The motif of mistreatment
Look at the various ways Bernadette ends up being a scapegoat in her daily life: She is blamed for running over someone's foot, when she didn't do it. Her husband blames her for his marital boredom. Her architecture is destroyed by a jealous neighbor. Her favorite assistant is a spy trying to rob her of all she's worth. By the time Bernadette disappears, she has a long list of reasons to run away, and each of them is essentially the same—people use her as scapegoat for whatever is wrong in their life. She ends up tired of that mistreatment and so she frees herself of those social burdens by leaving.
