We already have two skill tracks: individual ship boosting skills (those officers can take) and fleet boosting/ability adding skills(those officers can't take). I propose chopping the skill system apart along those lines.
I think its fundamentally unsatisfying in a game focused on flying our spaceship and blowing up enemies for the individual ship boosting skills to be suboptimal - the player should not be worse than the officers at boosting their own ships unless the officer is higher level than the player. "Officer Envy" is real and bad.
At the same time, if the single ship boosting skills are too powerful it skews combat greatly towards just deploying ships with officers, max combat skills, and then always picking the same few 'must have' other skills (see .7.2 skill balance). Finding the sweet spot between 'super ships away!' and 'strong fleet, weak player' is a difficult design job that changes with any new feature. (Not to say you can't do it, but hard is time consuming.)
With that in mind, I think the skills system should have two types of points. Officers get individual ship boosting skills. The player gets both an individual and a fleet-wide each level. I'm on the fence about aptitudes - I get that they are supposed to make player specialization more optimal, but I don't think they work as they are right now.
A huge advantage of two types of points is that it separates the balance between the two skill categories. Individual ship affecting skills can have different power levels from fleet wide skills and it doesn't matter, because they no longer compete for points (Combat Endurance 3 vs Fleet Logistics 3 wouldn't be a problem). The balance between officer/non-officer combat ships can be tuned easily without messing with anything else.
UI wise, you could recycle the current look by turning the aptitude area into the number of points available for that type of skill.
Its also an extensible system: Maybe there is another point type for colonies that has the administrator skills? Maybe the different types of points are tracked separately, and you level each with different activities?
Well that turned a bit long.
