The importance of relationships
The most obvious and important theme of the novel is that by opening oneself up for vulnerability and companionship, sometimes the perfect friend comes along, and although that doesn't mean life gets any easier, it does mean that the person doesn't have to be alone in their struggle.
Another important aspect of relationship is that we learn through loving other people that other people's experience often helps them to understand how we feel. This is Amy and Matthew's discovery, finding out that even though they never expected to meet someone who understands what it's like, they actually do understand each other. They're not alone.
Life with inhibiting conditions
It's easy to skip over the real struggle of daily life for those with conditions that limit their abilities in some way. Although both are intelligent and capable, Amy has a hard time communicating effectively with her voice box, and Matthew finds it impossible to keep his mind from wandering into various compulsions. Therefore, their lives are more arduous, and the same demands of life on them is more costly, because it takes more energy and time for them. However this is not to say that their lives are worse, because they have each other, which is nothing to sneeze at.
Falling in love
Love is what people make it out to be, no doubt, but even so, the teenagers in this romance experience something very sweet indeed. For them, love means that they don't have to go through life alone anymore, that they can be understood, even though they are each locked into unique, challenging lives—at least they will have each other for companionship and support.
