I remember talking to someone a bit ago (someone with considerably more experience) who said that theme is pointless. A writer shouldn't think about it once during their work. It's just a word used by critics and academics. A prestige thing. To which I say - bollocks!
For me theme is what makes a good movie (which may have a very enjoyable story) a great movie. Particularly with sci-fi.
2001: A Space Odyssey is a classic example. Some say it's only about theme and that there's no story whatsoever. They may be right, but in terms of theme, it's littered with interpretation. "Bring your own subtext," as Joss Whedon would say. I've read/heard about dozens, if not hundreds, of interpretations of 2001. What is that Monolith? Is it God? Is it an alien being? An alien technology? Does it merely symbolise technological advance? Organic advance? Change in human life?
Take one route.....
The monkeys open the film. They are at war with a rival clan, it's a stalemate. One monkey touches the Monolith. Then he uses a bone as a weapon to win the clan war. The Monolith triggers his development into the humans we see aboard the spaceship. These guys also encounter the Monolith and x years later, the ship is controlled by the computer HAL - technological evolution. The people aboard this ship are forced to kill HAL, the thing they created. They destroy their own technological advance. Dave encounters the Monolith again and ages dramatically - the Monolith destroys human life and gives birth to the next stage of evolution (whatever we see floating in space). Theme = technological and human evolution.
Another interpretation: the Apollonian vs Dionysian man.....
The monkeys are purely Dionysian - instinct, emotion, the "id" - and that just doesn't work, the result is murder. Later, during the Jupiter mission, the characters we see are purely Apollonian - structure, logic, the "ego" - having created a mechanical being (HAL) to control their lives. They are completely devoid of emotion and what makes humans human. This also fails, resulting in death. So in the film's finale, the Monolith scraps both versions of Man (Dave ages rapidly and dies) and creates a new form (the foetus we see hanging in space is another kind of Man). This is the "super ego", the natural balance between the instinctual, primal side of Man and the logical, mechanical side. What Freud would say is the balance needed for humankind to function completely. Theme = what makes us human?
Anyway, those are just two possible interpretations (very loosely summarized). The point is, you can throw anything you want at 2001 and it will stick. A religious interpretation - the Monolith is God and He presses the reset button on humanity. Or.....in the end, Dave - the representation of Man - becomes God (he is afterall, hovering in the sky over the world all deity-like).
One way of creating theme would be to write the script (forget about everything else). After draft 1 or 2, look for some sort of interpretation for your script, and you can create a theme. If your film has a clear Christian vs. Atheist thing going on, change that character's name from Bob to Abel. You might surprise yourself....
Next up - Blade Runner.