Gotta say the "junior officers" idea strikes me as a good one. And would work on in a variety of settings--starship, space station, colony, etc.
I had this notion for a character, a half Vulcan/half Andorian. Partially because I rather like the idea of someone who looks like a blonde Vulcan with blue skin! But the more I thought on it, the more it seemed the strength of this idea is of someone who embodies a taboo. These two races have been historical enemies and in most ways seem total opposites. Even their homeworlds! One an arid desert, the other a frozen wasteland. One has no moon, the other IS a moon. But more than that, Andorians evidently have four genders. This person, this halfbreed, what gender might they be? Quite possibly something...unique. More, doesn't this mean this person must be the result of genetic engineering?
I suppose the idea of this character appeals to me because she (to pick an arbitrary gender designation--and with a note I want to see more female characters) can work as a magnet for prejudice. Not merely because she's the result of a defacto forbidden union--with Andorians and Vulcans both reacting to her poorly--but as the recipient of false expectations. People would see her behavior solely in terms of her heritage. If she remains calm in a crisis, it isn't because she's developed personal discipline it is because of her Vulcan blood. When she holds her own in a firefight, she's told "Must be the Andorian side!" A subtle but pervasive prejudice, one much more likely to show up among her fellow junior officers since they're less experienced. Yet ironically they're also the ones most likely to (eventually) see her as an individual through constant interaction.
To really work, of course, she needs full development as her own person. Not simply a collection of quirks or details, but a dynamic whole. I know someone who once insisted Honor Harrington (of the David Webber series) is a fully developed character because "she has that Treecat!" *rolls eyes* Although that character does seem to me to have gotten rounder over time--my image of her now is as a wild wolf in human form, but governed by a mighty intelligence and emotional bonds to the humans around her--she still isn't nearly as full as (for example) Esmay Suiza in Elizabeth Moon's Once A Hero. In terms of space opera television, I would point to Aeryn Sun or Chiana on Farscape, Starbuck on the new BSG or Ivanova on Babylon 5. Someone with that level of depth but as a very junior officer and with this baggage of subtle but pervasive prejudice surrounding her.