The biggest lesson readers should take away is “imagine others complexly,” to quote John Green himself. Specifically, Paper Towns accomplishes this by dismantling the common “manic pixie dream girl” trope.

Since childhood, Q has seen Margo as a sort of magical, mysterious presence. While he does not know her intimately, he has an entire “imagining” of the miraculous Margo in his head. After their night of shenanigans, the usual manic pixie dream girl story would maintain Margo’s mystery and utilize her as only a plot device to deepen Q’s sense of self.

Instead, Q spends the rest of the novel on a quest that unravels the imagined Margo, replacing her with a less glamorous but more honest version of herself. By the end of the text, readers have deeply explored the benefits of imagining others complexly and the dangers of not doing so.

Lessons on perception are also included in plot elements beyond the central conflict, like Radar’s parents’ collection of black Santas. This detail asks readers to further examine a common, typically unexplored cultural image.

Paper Towns is peppered with various life lessons.  The main overarching theme of the book is that people are rich and complex and have sides to them that the average person may not see.  It's disingenuous to assume that you know everything about a person when you aren't close to them.  Quentin believes that Margo is a miracle who will make his life interesting and save him from mediocrity, but Margo is a girl with her own troubles who barely even knows herself.  Quentin learns that he needs to treat people as complex human beings rather than concepts, and that he needs to rely on himself to make his life interesting rather than relying on other people.

The importance of friendship is also stressed throughout the book.  Quentin's friends support him.  A third of the book is about the adventures he and his friends have on a road trip together.  The book stresses living for yourself and living in the moment above living for the expectations of other people.