I think the underlying theme is "evolution". The movie seems to revolve around questioning the existence of God.

But in the end.. It is us human that created the Xenomorph. It all started with David dropping that black goo into Charlie's drink. And the first stage of evolution took place within Charlie. The second stage is when Elizabeth is impregnated and out came the squid-like alien. The third stage is when the alien planted its egg into the Engineer. And out came a Xenomorph-like creature, which I think will go through a couple more stages of evolution until it eventually become the Xenomorph. In short - "A lifeless form (David) created a new life form (the Xenomorph)."

If you remember there was a scene in the room with the big head statue, where they showed worms on the ground. Milburn & Fifield encountered a snake-like creature in the same room, which I think is the evolved version of the worm.

And so the Engineers may have visited Earth millions of years ago. And the same evolution cycle, like mentioned above, may have created the human race.

Everything else, is just meant to make it a watchable movie, without being philosophical. Alien wants to destroy Earth, we must stop the alien. Bang bang boom.

My 4 cents worth of opinion.

Charlize Theron as Meredith Vickers is a tad dissapointing. I can't tell if she's an antagonist in the film. Idris Elba as Janek the captain had one line that aptly capture her characteristics in the movie.

Janek: Hey Vickers, Vickers.

Vickers: turns around...

Janek: I was wondering.....Are you a robot?    

I love Charlize Theron. She just looks so cute in her scene, but the character just doesn't fit her that well. Being the corporate daughter of Peter Wayland, she had like a love-hate relationship with her father, but at the same time, she is this hard-stance, b*tch-cold boss in the Prometheus. In the end, she lost all that when Weyland emerges into the scene. Now she is this lonely, unwanted daughter who lost the respect of anyone and even lost control of the ship, and finally ends up a pancake on a distant moon pinned down under an alien spaceship for millenia. How depressing is that?

As for the timeline, Prometheus happened between 2089 - 2093 while Alien 1 happened in 2122. There is still the possibility that the sole alien queen in Prometheus hitched a ride in another alien spaceship and crash landed in LV-426 where Ellen Ripley first met the species. Most of us might be trying too hard to connect any relation between Prometheus to Alien 1 story arc, but its also plausible that both story just happen in the same universe without ever crossing path each other. Meaning to say that the queen alien from the 1979 installment came from a different origin entirely while the queen alien in Prometheus is a different breed.