This is not really a fair question because this book has so many lessons to teach; however, in my opinion, the main lesson of Freak the Mighty is that friendship and platonic love can breakdown many barriers.
At the beginning of the story, Max has low self-esteem, feels unloved by his father, and deems himself completely unintelligent. Likewise, at the beginning of the story, Kevin suffers greatly from his birth defects (both with his small stature and his limp) and lives only in his imaginary worlds.
Things change for the two boys because of their platonic love for each other. Together, the two become the unified "Freak the Mighty." Max learns that he is both incredibly smart and brave, able to combat even powerful criminals like his father, Kenny "Killer" Kane. Kevin learns that, although he cannot change his physical deformity, he can completely overcome it by being friends with Max. Kevin can now move quickly and with strength as "Freak the Mighty." Further, through the boys' adventures, Kevin explores the real world instead of just living within his imaginary world.
The beauty of friendship transforms the pair of boys. Although Max struggles with Kevin's death, Max emerges as a stronger person than he ever was before, able to write down the stories of Kevin and Max as "Freak the Mighty." These stories (the ones found in this book) are a testament to the power of friendship and platonic love.