I tend to ignore the whole US Military thing myself. Sure, it took inspiration, because Rodenberry was ex military. It's what he knew. I know nothing about military life and I don't want to write about that. I base it on what we see on screen, and my own slant. Every trek series showed this. A new ship with a new crew starts off regimental, with everyone just feeling each other out. But after a couple of years, it becomes less like a military vessel and more like a road trip with friends and family. You become comfortable with those you serve with. I'm sure a military troop, while also having similar feelings, doesn't let that family aspect show the way Trek ships do. So instantly, there's that. Also, Starfleet has different regulations to the military. Just ignore the actual specifics and make crap up to suit what you want to write about. It's what I do. And if you don't want to write painstaking detail about that style of life, don't. It'll be boring for you to write, and will come across in your writing so the reader will get bored reading it. You may notice I barely use my crew's doctors in the stories, or explain about how they're healing them. THat's because I don't like writing about medical procedures. I don't have much knowledge on it, and I find it detestably boring. Yes, it means Bob Juffra is severely underused, but it means I don't write things I don't want to. If someone writes a good procedure, I'll happily read it. But I will not write it.
.Though that might still change in the future if I do manage to stop thinking "army stories" every time I think of Star Trek stories!
This right here needs to change. Trek stories are not war stories. They were never war stories. They are stories about humanity. About pushing ourselves in the face of adversity, about looking into the future and seeing what's out there. Or sometimes it's just a crazy fun story about stopping thousands of balls of fluff that never stop breeding! Heck, even when they actually had a 2 year war, the stories were more about the characters and how things affected them rather than the actual war.
I know people on the STO forums say write a bit every day, even if you don't want to. I would say don't. If you don't want to write a story today, don't. You'll just be wasting your time, as I find I write very flat pieces when I do that, and end up having to spend longer going over and reworking them at a later date. That first Transformers crossover I wrote, that was sitting on my hard drive for about 4 or 5 months getting smidges added to it here and there before it was completed. But I was very happy with the end result. If you don't want to write in the Trek continuity, don't. Take a break from it. There are plenty of other worlds you can try writing in. Put Ellen in Firefly's verse for a spell and see what adventures she comes up with there. Keep her the same character, but dropping her in a different verse could help you flesh out the character a little more, as she'll come across things she otherwise wouldn't. Afterall, Stunshock started life as a red shirt in the very first proper story I wrote, which was a Transformers story. It was literally introduce him, have his team get killed to show how powerful this big bad was. Then I decided to do a sequel set many years later where he had actually survived, and went on his first real adventure, giving him some actual characteristics. Which then came into play when I brought him into a TF RP on a board.
And many of those aspects of his original character are still seen in his Star Trek incarnation. I waffled a bit there, but my point is, if you don't want to write trek stories, dont. Try Firefly. Or put her on Caprica when the Cylons attacked. Or have her at Hill Valley on November 12th, 1955 where she runs across someone running a weather experiment in the street. Or she's in the Old West where she comes across a town under seige. Does she try to help the townsfolk fight back, or does she try to make peace?
Or do a story set entirely on an away team. You have your characters, but they're on an alien world. No trek setting needed. It could even be one of those parrallel Earths that Kirk was constantly running into. If you get ideas, and you want to write a story, just start writing it. Don't worry about how little sense it might make at the time, you may come up with a way to explain it by story's end. Or you mention it in story as being weird, the characters know it's weird, but no one questions it because.... well, it's weird. Or it turns out to be a dream. And we all know all rules are off in dreams.
I view it more as 'Imzavia is a Captain for the purpose of this posting' rather than Emony going down a rank. Emony is the only full Commander on the ship, but she's accepted the posting knowing she's going to be under a Captain who is a rank lower. Imzavia will introduce herself when making ship to ship meetings and so on as 'Captain Imzavia', but at formal Starfleet functions/meeting the top brass, she will be introduced as 'Lt Cmndr Imzavia', as that is her official rank in the fleet. I've seen it on TV shows where someone of a lower rank can boss those of a higher rank around because they are the mission specialist. Heck, I seem to remember a TNG S1 episode where there was an Admiral on the ship, but Picard was still commanding the Enteprrise and made all decisions there. The Admiral only took charge once they got off the ship.
And thank you. I do like knowing folks are reading my work.