I *really* like the crew aspect of this game. This is likely to be one of my favorite parts. I like Bluddy's suggestions, except for the specific crew vs. specific crew. I'd change that so that:
a) Crew have particular kinds of missions they like. Certain kinds of missions will be opposites, likely (or close enough) so that they shouldn't both be liked by the same crew. But this I think gives you more flexibility than the "Good vs. Evil" axis.
b) Crew that have opposite preferences may come to dislike each other. Feuds among crew should be either i) a test of your leadership--how do you adjudicate as the captain? or ii) an encouragement to be consistent with kinds of missions, so that if you want diversity, you need to do more management.
Also, in addition to bigoted crew, maybe it'd be a good idea to have multicultural crew--crew who like serving with different races generally, crew who like to work with particular races in addition to their own. And of course like Bluddy was saying: Crew who are mission oriented. Crew who are money oriented. Maybe crew who favor particular parts of the galaxy (or maybe not--that might be too complicated).
Anyway, I really like where you're going with this.
One concern I have--I really like to be able to have my crew in games like this be loyal--as such, I feel compelled to treat them well as loyal members of my crew, and thus limit arbitrary firings just to optimize my crew. I know this contradicts the gameplay in Depths of Peril--which I could deal with, but didn't like. I'm hoping that in this game you can put effort into training and developing crew, so that you can build their loyalty, and not have to shuffle them around like engine parts. I'm fine with shuffling around tech. I want to have long-term relationships with crew.
Now, if it turns out that your mechanics require crew to be swapped out, I understand, but then can I request that you give me other options for getting rid of crew besides just firing them? Can I maybe send them off to a training school? Set them up with their own ship? Find them a new job with a friendly captain of another ship? Get them a cushy job on a space station or planet? Or something? I guess this would also suggest that airlocking problem crew (with appropriate effects on happiness, discipline, etc.), or abandoning them on remote planets should also be an option. For the "good" options, I don't mind if I have to pay some money to get rid of a crew member who I consider valuable. Another mechanism is that you could have a crew contract system, where you specify how long (missions? game time?) a crew has a contract with you, and then you can renew it when it expires, or just let it expire. This could be one mechanism for setting rates of pay, frequency of pay, etc.
I assume that the player is not the only Drox Operative at work in the game? And perhaps that Drox Operatives are not the only independent operators in the game?