Manipulation and control
Every adult in the novel shapes Ender's environment to produce a specific outcome. Graff isolates him, changes the rules, and uses Valentine against him. The theme asks whether a good result makes this kind of control acceptable, and the novel refuses to give a clean answer.
The cost of genius
Ender's intelligence makes him valuable and makes him a target. The teachers push him harder precisely because he can handle it. His gifts don't protect him; they expose him to more pressure. Card shows that being exceptional doesn't mean being safe.
Moral responsibility without full information
Ender commits genocide without knowing it. The novel forces the question of how much a person can be blamed for actions taken in ignorance, especially when that ignorance was engineered by others. There's no comfortable resolution.
Empathy as both strength and weapon
Ender understands his enemies so completely that he can defeat them. But the same empathy makes him grieve for the Formics once he understands them. The teachers use his empathy as a tool. Ender eventually uses it to seek redemption.
Childhood and the loss of innocence
Ender is six when the novel starts and still a child when he ends a war. He never gets to be a normal kid. Card makes this concrete through small details: Ender's loneliness, his need for Valentine, his breakdown after the final battle. The military takes his childhood and calls it necessary.