I'd like to see in addition, more ship officer positions. Science officer, Chief Engineer, First Officer, etc.
I'd imagine with a few of these, you'd see new bonuses as well, such as Damage Control Bonus, MSP usage reduction, random chance that ship components are treated as 1 or so HTK tougher, crew casualty chance reduction, boarding combat bonuses (against boarders), etc.
Not sure what the science officer would do. Increase the science yield from salvage operations perhaps?
Just thought of another bonus the Chief Engineer could give: Life Support Tenacity Bonus. As long as the commander remains alive, the carrying capacity for life support until dangerous failures occur is higher based on their bonus. Makeshift life support systems will meanwhile last longer based on their bonus if it comes to that.