Children's Competency
Children know exactly what is going on, and they are much more capable than the adults in their lives often think. Claudia and Jamie are able to successfully penetrate the security of one of the largest museums in the world for a substantial period of time, something that many adults would be unable to do. Problems arise when the adults in children's lives do not recognize the children's intelligence, and do not treat their competency with full respect.
Middle-class Dissatisfaction
In many ways, Claudia Kincaid has it all: she has a stable family with a comfortable home, and a decent allowance as well. However, she is deeply discontented with her life, and eventually runs away. As a teacher in an upper-middle-class school, E.L. Konigsburg noticed such widespread dissatisfaction among many of her students.
The Value of Money
Since Claudia and Jamie are running away, they must be very careful of the ways they use their money. Each purchase must be carefully considered, and any superfluous expenses (such as taking a taxi when they could easily walk) must be vetoed. It is money that allows the children to live safely in New York for a week.
Given the emphasis on money and the careful budgeting exercised by the characters, this book could be an excellent way to teach children budgeting and basic financial math.
Art
Claudia does not just want to run away from something, she wants to run to something - and she decides upon the Metropolitan Museum of Art, a glamorous museum that suits her tastes. The children are able to tour the museum filled with priceless art, and eventually they are drawn into the mystery of Angel, a statue that Michelangelo might have carved. The beauty - and often the mystery - of art permeates the book, and eventually allows Claudia to achieve her goal of feeling truly different.
Grammar
Claudia and Jamie frequently argue over the use and misuse of grammar – for example, whether or not the phrase "run away to" is grammatically correct. This leads to a light and humorous mood, and also subtly draws the reader's attention to the language used in the book.
Family
Members of the Kincaid family, despite being related to one another, are not particularly close. It is only when Claudia and Jamie depart on their adventure to New York City that they truly become family - close, supportive, and loving towards each other, despite their frequent arguments.
It's not just blood that makes a family. Mrs. Frankweiler becomes like a grandmother to the children, despite not being biologically related to them.
Feeling Different
More than almost anything, Claudia wants to feel different - different from other people, and different from herself. She loves feeling unique and special, and she also wants to make sure that she returns home a different person than she was when she set out on her adventure to the Metropolitan Museum of Art. She is able to achieve this goal after her interaction with Mrs. Frankweiler, who knows how wonderful it can be to have a secret that no one else knows.