There's this unrealisticness that comes in a lot of the Sci-Fi episodes that I've seen. Like in OG Star Trek, Captain Kirk goes away on dangerous missions away from the ship. That's unrealistic.

- food comes from replicators

- people travel faster than the speed of light

- you get to the planet by "beaming"

...and it's the org chart that has you upset?

Nope. Sorry, bud. Sticking to my guns on this one: you have a preconception of the way people are supposed to act and you refuse to extend suspension of disbelief to the show because of it.

The USS Enterprise may be a big goddamn space ship but it's run a lot more like the PT109. There's a crew of about eight people who matter and then assorted fillerfolk who tend to die. It's literally Wagon Train. That you've got your head wedged about "captains don't do this" or "military men don't do that" says more about you than it does about the show - did you miss the part where O'Brien's wife and kid are there on the space station with him? And how is it that an alien space station tidally locked next to a wormhole gives you no pause, but a shift in military doctrine over the space of 500 years is the Rubicon you will not cross?

That's all you.

So yeah, I'm still saying, if you're gonna bring up shit for the sake of exploration, explore it.

You're not, though. You're saying "I want to talk about the loopholes you're invoking that make me uncomfortable, not the stuff you wrote the show about." And that's typical of sci fi fans, by the way: god help you if there's sounds in space but of course aliens have boobs. This is why they are largely ignored by the market; fans of television will consume television. Fans of sci fi will consume stuff if it's only just so and then bitch about it on internet forums about how inaccurate it is. Actually, that's a lie. Hollywood knows the nerds will watch anyway and doesn't give a fuck if they bitch.

I think the best analogy I can come up with so far is if the Brooklyn 99 team found a time bomb in their office, acknowledged it was there, and then left it as a central part of the plot without actually trying to figure out where it came from, how to get rid of it, or anything of the sort.

A better analogy would be to state that the Brooklyn 99 team found a time bomb and determined it was harmless and then moved on to other things. Remember - it is accepted as the fundamental basis of the universe that people can be constructed out of mutherfucking light with exquisitely perfect accuracy. If you're willing to accept transporters and replicators, you have to accept the notion that a medical scan is fuckin' final. Those are the storyworld rules.

This is a big part of writing - determining the storyworld rules and working entirely within them. This gives your narrative the consistency your audience demands: generally, if you say "elves live forever, a palanteer allows you to see across the land and orcs are half-men, half-goblin" people accept it and move on. Platform 4 3/4 or whatever gets you to Hogwart's and if your wand breaks you lose your mojo.

You're not accepting the storyworld rules.

That's fine. Sci fi probably isn't for you. But stop trying to justify it as a problem of the writing rather than a problem of your enjoyment. Again, Season 1 DS9 ain't great. But it ain't great for reasons utterly unrelated to the justifications you're pulling out of your ass.