You know, the idea that's been bouncing around in my head for a really long time, is that of the crew of a space frigate. Not like, rah, rah, Star Trek, but more like Master & Commander. Maybe told from the point of view of the 1st officer, so that the reader gets more sense of the operations of the ship, as well as command.
I'd like to see the Captain be brave and resourceful, but also a bit old and fallable, with a young, pretty, neglected, naughty wife that our 1st Officer hero could get connected with during shore leave. Then, when they go to war, our hero will have something to really worry about. Right there, you've got some nice conflicts: Man vs Man, Man vs. Woman, Man vs. Himself, Man vs. Slimy Tentacle Alien Beasts That Do --- Oh, Auughh, I Can't Even Bring Myself To Type That!!
Maybe the Captain gets killed half way through (I call it the Sameul L. Jackson Effect, from "Deep Blue Sea"). Maybe the war ends, or worse, goes suddenly very badly, and our brave ship gets captured. Then there's the stirring finale.
It's not exactly GalCiv material, but it could be adaptable. There is a LOT of room in GalCiv for all kinds of personal stories. I remember getting all fired up about the in-game message how a salvage spaceship captain in GalCiv2 found a 1BC coin in some ship debris. He says, "This must be my lucky day". If I found a coin worth 1BC lying in the trash, I'd probably just stroke out. "Arrr-Arrrgh," he said, as he popped his head gasket.
The GalCiv2/Stardock pixel monkeys went to a lot of trouble to come up with humour in this game, and I like the little jokes a lot. I'd figure that if I were writing fan fic for this game, I'd want it to be at least a bit funny.