Because of sheer volume of output, science fiction is generally considered to be an American genre. But good science fiction transcends national boundaries. It's universal.
Look at Stanislaw Lem, author of the excellent Solaris. Lem is Polish and wrote the story in Polish, but in no way do we consider Solaris to be a simply Polish science fiction novel. We are so drawn into the suspense of the story that nationality becomes an insignificant distinction. Solaris is a haunting psychological thriller that explores universal human condition, as well as a fantastic addition to scifi canon.
So what then? Should we stop writing Filipino science fiction in favor of scifi of the more universal sort? Certainly Filipinos should aspire to write good science fiction, but I don't know if it's possible for Filipinos to altogether stop writing Filipino science fiction. In a sense, any science fiction that a Filipino writes still is Filipino science fiction.
There's an old admonishment: "write what you know." That's just as true in science fiction as it is in any other genres. Never mind that we're writing about the human race in the year 40,000 or about an alien virus. Being Filipinos, any work we produce will be infected with our Filipino sensibilities. The closer to our true sensibilities, the better the work. The best way to express a universal human truth is to express the truth that is closest to us.
Returning to Solaris, astute readers will notice a subtly different flavor to the narrative and the characterization as compared with American scifi stories. There's a brooding quality to the entire novel. The primary focus, you see, is not in the exploration of the planet but in the protagonist's relationship with his back-from-the-dead wife. This is something that we might attribute to the Polish-ness of the author.
If a universal truth by way of a Filipino truth is the aim, then some science fiction stories must necessarily be written in Filipino, that is, in Tagalog, Bisaya, Iloko, etc. We may write perfectly grammatical and impeccably idiomatic English, but some emotions and sensibilities can only be authentically expressed in our own language.
Solaris, again: the novel was written in Polish and Lem has gone on record to say that he was never truly happy with any English translation of this work. This hasn't stopped Solaris from being a moving tale for English readers, but one wonders how much more insight and depth we might gain if one reads it in the original.
In the end, we go back full circle. At the heart of the argument: a Filipino science fiction story is a science fiction story that expresses some fundamental truth about Filipinos. By varying degrees, the other accidents follow in due course.
How can you express the truth about Filipinos if you are not Filipino yourself?
How can you express a deep truth about Filipinos authentically if you do not do it in the language of thought of the Filipino?
How can you draw out the truth about Filipinos in fiction if not with the use of Filipino characters?