Communication
For Amy, communication is difficult and tedious, and what's worse, she knows that she is boring to people just because she has to speak through a speaking system, instead of with her mouth. This voicelessness is solved when Matthew understands the same challenge, but in his own way.
Intimacy
Compare Amy's failure to make friends with her willingness to fall in love. Her constant frustrations regarding friends have left her lonely and willing to see the best in anyone who will pay attention to her. So when the lovers meet, there is a quick development of intimacy, ironically due to their lack of intimacy in other arenas of life, and the fact that their challenges make them emotionally compatible.
Ability
The novel describes intelligent, winsome teenagers with a backbone. They aren't weak or stupid, just because they're differently abled. In fact, some might say they are better suited for the difficulties of life than those who get through high school with ease. So there is an ironic confusion around the couple's ability—just because they are limited in some respects doesn't mean that their experience of life is less beautiful, valid, or meaningful. After all, they seem to have found a pretty sweet little romance for themselves. That's a demonstration of their willingness to serve each other, something others often take for granted.
Dependence
The philosophical response to the novel might be, "Is this dependence?" but the answer to that would be no. Just because the two trust each other and rely on each other for moral support and company, their lives still belong to themselves respectively. For instance, when Matthew supports Amy about the challenges she faces making friends, he just encourages her. Likewise, Amy doesn't try to control Matthew, but rather, she listens and understands his difficult mental health issues. The relationship is relatively healthy, which is an ironic feature of the novel, given that mental health is an subject of discussion.
Chronic health issues
Although the limitations of chronic health issues like cerebral palsy or OCD are not unnecessarily painful, per say, the way they change a person's ability does cause them suffering, sometimes extreme suffering. For instance, cerebral palsy patients and OCD patients both are more likely to sink into severe depression. As the book so eloquently captures, even basic human actions can be difficult, like making friends, or studying for a test. Chronic health issues are deceivingly complex.
