This actually gave me some good insight. Ive still been plinking away at building my deep-space campaign, and I've sort of been avoiding doing any work on the story in favor of fleshing out a few characters and doing more worldbuilding. I think I have a good idea of where I want to go, but I also want to develop my encounters in such a manner that the players don't feel forced to one particular investigation over another.
Just a thought, how does everybody make their villains? I don't mean just mean antagonists, but really good hate-able characters. I always try to start with the maybe cliched 'Every good villain is the hero of their own story' and go from there. Maybe not as elaborately as that example, but same kind of idea.