Science Fiction itself does tend to fall into categories of its own. You've got 'extrapolative science fiction', which bases its tales on the 'What if?' method of story generation. What if we could create androids that were indistinguishable from humans (Blade Runner)? What if we could travel backward through time to prevent disaster (The Terminator)? What if the world as we know it turned out to be a fantasy occurring only in our minds (The Matrix)? All very famous stories, yet only The Matrix was made into an MMO, and by all accounts, not a terribly successful one.
Then there is Space Opera, the most enduring and popular exemplar of which is Star Wars. Featuring larger-than-life characters, events, and set pieces, this is merely Fantasy with technological trappings. Is Star Wars Galaxies as successful as it could be? Only slightly removed is Military Science Fiction, under which banner we can include Starship Troopers. Tabula Rasa is the most obvious connection to be made here, though you can also include Eve Online -- while its ships are not specifically military, ship-to-ship combat is certainly familiar Science Fiction fare.
Of more recent pedigree is an offshoot of Science Fiction called Cyberpunk. This sub-genre features high technology being employed at the street level; good examples of Cyberpunk stories are Strange Days, Johnny Mnemonic, and, possibly, Max Headroom. This subgenre at least provides a gritty, urban environment in which to base stories of all different types, but its contribution is merely that, and perhaps a dash of attitude. Add Neocron Online to this.
If there is a running theme throughout each type of Science Fiction, it could arguably be that of Wish Fulfillment Negated. At first, a Utopic idea is floated, with the outcome appearing bright. Over the course of the story, however, it becomes clear that complications will arise, almost in direct opposition to the idea itself, with a moral lesson to be learned: Be careful what you wish for -- it's not what you think it is. If that is the prevailing theme of Science Fiction in general, is it any wonder that there are few notable Science Fiction MMOs?
If we can take lessons from arguably the most popular MMO of our time, World of Warcraft, we can see how it compares, thematically: The world is filled with conflict, but there is honor. A hero may rise from humble beginnings to become mighty. With the use of magic, one can accomplish miracles. There is an almost ridiculous positivity at play here, in direct opposition to Science Fiction's more sober truths. Simply put, it's just more emotionally rewarding to play a hero, accruing power and prestige, then there is in playing a nondescript cipher, coming to terms with the fundamental nature of the universe. Whether it's openly stated or not, Fantasy carries within it the chance to win everything, while in Science Fiction, the goal is to understand. One is not necessarily more valuable than the other in moralistic terms, but certainly easier to turn into a game design document.
Obviously, this doesn't preclude a great WoW-level Science Fiction MMO being created, but whatever's on its way, it certainly has its work cut out for it.