Again, I absolutely thing trans people, identity, and issues should be represented more in media - even in fiction. I'm just not sure it makes sense to depict all of this in all science fictional stories.
I mean, to give an example, in The Culture series of novels by Iain Banks, nearly everyone freely switches genders over the course of their (long) lives whenever they feel like it. The main character in the novel Player of Games is explicitly singled out for being somewhat weird because he doesn't want to transition to be a woman for a period. Since 90%+ of people are what we would consider trans (at least at some point in their life) the idea of a discrete trans identity doesn't make much logical sense, because the idea of concrete genders doesn't make much sense. People aren't male or female, they just take on that role for a period until they get bored, then switch things up.
I guess it comes down to what kind of sci-fi you prefer, to some degree. I kind of prefer that far-future sci-fi show a culturally alien landscape rather than just be a mirror held up to the present. If we want that, we can use a near-future sci-fi setting instead. This is one reason it's always irked me that Star Trek has always been fairly decent with racial representation, but shown very few interracial humans. The logical conclusion of centuries of humans living in a post-racist era, constantly moving around, is that most people will be racially ambiguous, not easily slotted into the current "races."