Science Fiction is a mirror of what we find in our current state. The human animal is capable of more and more advanced thought and technology. The last 150 years is proof of that. But the animal itself--the need to be loved, to be fulfilled, to find peace and happiness, food, shelter--are as true of our caveman ancestors as they are of ourselves. Science Fiction is the juxtaposition of those two realities. They can be in tension. For instance, cellphones are mini computers and keep us connected through the written word, but less connected to the people we are around when the cellphone is taking up our attention.
With all stories, start with what you want to say. It can be complex and focused (your opinion of an aspect of human society), or a more universal concept (like finding love and the barriers we face when pursuing that love). Build characters that are realizations of this vision, contrast each other when compared, and make sure it is a true and interesting story. The best fiction--whether set in the past or the future--connects to those needs I described above.
From there, tone is important. Edgar Allan Poe, the founder of the modern gumshoe stories and the macabre science fiction, was able to have definite changes in the tone of each story when compared to another. Stephen King is good at this as well, the unbelievable representing a monster we find in our real world. Joss Whedon, contrasting that, built a backdrop that is dark, but a hero that shone light on it in
Buffy the Vampire Slayer and used those stories to be allegories of aspects of growing as an adolescent into adulthood (and he managed to infuse a lot of humor into his backdrop). Gene Roddenberry saw humanity evolving into its technology and outgrowing our painful emotional states in
Star Trek.. Pick a tone, one that fits with the story and what you want to say, and stick with it.
There's not much difference between good science fiction and other literature except for the need to explain the world because it is foreign to us. Some ways to explain, like having each character guess and come up with a theory, is outdated and not good fiction.
And example for all of what I see as good Sci Fi: Take, for instance,
Super 8. We don't know the monster's motivation until we see the Scientist that was killed at the crash site talking about his psychic abilities with this creature. He just wants to go home. What the movie is about is loss. Without the main character losing his mother, he never makes a connection with the monster telling him "bad things happen." Losing his mother saved his life. That was momentous synergy in the script. They managed to write a scary story from the eyes of a child, and an interesting one, without beating us over the head with the fact that bad things happen, and people need to be forgiven for doing terrible things to you. That's the best JJ Abrams film I have ever seen, including the Star Trek movies.
I don't feel like I've got all my ideas down in this post. I feel something is missing, but know that I tried to
write science fiction in the Fan Fiction section. The story that I did spoke to me, even if it didn't speak to anyone else. It talked about our current political climate, the nature of freedom and what it truly means, and growing into yourself (and feeling the loss of that character when her life is snuffed out. She left her life unfinished). I don't know if it was any good, but it felt good writing it. Other people determine whether it connects with them or not.