This book explores several complex themes that tend to revolve around a central focus on "survival."
Manipulation is an excellent one to explore. The book basically poses the question of whether it is okay to manipulate people if ultimately it ends up being for their own good. Ender is manipulated by the teachers at battle school (and command school), in order to become the best and strongest commander and ultimately, to save the world.
In turn, he must manipulate others who are within his command.
Further, this theme explores the idea of what price must be paid in order to win. Ender understands he is being manipulated, and he hates it. He also knows that he is manipulative, and hates that. He realizes such an approach to greatness means sacrificing relationships, but at some point, he must be okay with this, because he knows that the fate of the world rests on his shoulders.