The Theme is the Universal Statement the film makes about the Human Condition.
Hauge, in fact, calls the Theme the Premise (but again, this is reductive).
The Theme emerges when the Hero recognises the differences between himself and the Reflection and the similarities between himself and the Nemesis.
In An Officer and A Gentleman, Zack recognises the difference between himself and Sid - Zack won't give himself to others, whilst Sid sacrifices himself for others. The film makers highlight this throughout the film by showing Zack and Sid through Foley's eyes: when Zack completes the training course and sits alone, the argument between Zack and Sid over dinner (about their differences), Sid's DOR and finally Zack going back to help Seegar, at the expense of him beating the record for completing the training course.
Zack recongises the similarities between himself and Foley - Zack is made to acknowledge that whilst he won't commit himself to others, and give of himself, he is desperate for companionship and to belong. He's got nowhere else to go. During the training for jet crashing into water Foley quips: 'You'll like this Mayo, it's something you can do on your own.' So, Foley has recognised right from the start what Zack's Inner Conflict is, and repeatedly puts it back in his face. Zack finally realises he needs to change, and falls in line with Foley... given that after Sid commits suicide, Foley won't allow Zack to DOR, and accepts a fight.
So, were we to look at the story with just Zack, the theme would be:
We become better people if we give ourselves to others.
This is enhanced by the inclusion of Sid:
We become better people if we give ourselves to others but without sacrificing ourselves for others.
We can add a theme of honesty to this, if we take Lynette as a Reflection of Paula - Lynette is prepared to trap an Officer, by becoming or claiming to become pregnant, so that he will marry her and take her away from her life, whereas, Paula refuses to compromise herself and real love (it is insinuated that her mother possibly did this):
We become better people if we give ourselves honestly to others, but never sacrifice ourselves for others.
In the Australian film Lantana the overarching theme is Trust. In pretty much every scene Trust is mentioned, referred or inferred to.