One could argue that the theme of Ender's Game is military ethics. Specifically, the breakdown of those ethics during wartime. Few things about Ender's military training can be called ethical. He's taken from his family, isolated from his peers, and manipulated by a man later tried for war crimes and child abuse. His training is passed off as a "game," subverting the innocence and simplicity of play for military means. Ender unwittingly exterminates an entire race because his trainers tell him he's merely playing a video game, not commanding military troops. He bears the guilt of this xenocide for the rest of his life.
The training school is just the mise-en-scene for the gradual maturing of Ender. The theme of the book has more to do with looking with fresh eyes at our opponents--the reason for his success in the training rooms. It is his final realization that the Buggers are not enemies, but rather a culture that has a different way of living, and his final preservation of the new Buggers colony, that reveal the theme of Card's book. As in all Bildungsromanen, the point of the story is not the maturation process (that is just the vehicle for the social or philosophical theme), but what is learned about his society by the protagonist. Cf. Catcher in the Rye or Lord of the Flies.
One dominant theme in Ender's Game is the challenge of success. Throughout the novel, Ender is incredibly successful in Battle School. He has the best hand-eye coordination and is a skillful strategist and game player. With giftedness also comes the burden of envy. Ender's gifts and success do not necessarily bring him happiness or even contentment. The more he succeeds, the more the other students and even his brother Peter resent him; beyond the other children's obvious envy and resentment, Ender also finds himself being manipulated for his talent and abilities. Ender's Game is a lesson in the universal truth that being the best does not necessarily mean being happy.
I've linked to the themes page so you can get more ideas.
One of the themes is ambition and power. Peter manipulates the masses to influence them and bring about the situations he desires. Graff, with his power, manipulates Ender into becoming the perfect commander capable of making smart but ruthless decisions to defeat the buggers. Peter manipulates to gain power and Graff manipulates because he has power.