Since there's now character skills and aptitudes, why not add crew that provide a similar benfit? There might be Engineers, who improve weapon reapairs during battle and improve ship repair/hull mod attaching outside of combat. There might be a Logistics Officer, who adds command points or adds fleet points. Of course, just one one these crew wouldn't provide the same effect as an aptitude point or skill point. You might need more of each, perhaps 50 or 100 of them, to provide the same bonus. They wouldn't affect if you could add more skill points to an aptitude, though.
They also might not count as regular crew, so having 50 of them would not crew a lasher or a wolf. They also would need more crew ot cargo space to hold them, to house thier items that make them special.