I'm writing this review without having read the earlier comments, I'd rather give you my initial reaction - and I'll post responses to other comments as a separate post.
First my reaction to this simply as a short fiction tale:
I enjoyed it. The first two page pages (to the first break) did have me wondering, because that felt stilted (and yet that effect is not entirely out of place considering the nature of the protagonists). But by the end of that section I was sort of intrigued about where it was going.
I do feel as if the middle part of the story may need some smoothing over - I find it hard to give specific issues here, so I wonder if it just needs an editing pass (maybe reading it out to yourself). I'm not keen on the twin designations for the Mate/DEP and the Captain/DEP, I don't think it's really necessary.
I liked the ending (the last two sections). It seemed to fit very well with the lead up.
My reaction as a science-fiction fan (I'm not really much of one any more, but I used to be) is less flattering.
I think the story is a good length for what it contains. Not sure if that sounds odd, but too many science-fiction stories drag things out further than the central idea warrants, whereas I felt satisfied at the end of this one, that the end had justified journey.