The more I think about it, the less this skill scheme seems to be working as it should.
The problem with binary skills is that, well, folks will play the hell out of this game and a few obsessive enough might be able to work out which choices work best, making binary choices less ideal.
I mean they'd need to be more gameplay style enforcing but at the same time, some skills with rather niche applications (strike craft/phase) oppose more generalist skills (I mean, no player is going to be running a mainly carrier or mostly phase fleet, my experience with either is limited, though I've had far more carriers and battle carriers than phase ships, that while a pest or pain to dealth with, seem to need far more control and skill than what I have atm)
So, I think this needs serious rework, try to put the potential playstyle paradigms on paper and then work on how to skill for those and see what can be branching. And even then, still have some skill options rather than and or
I honestly think the aptitudes need a basic and advanced distinction, for instance the basic Industry skills could be all about trader vs scavenger and the advanced ones mostly colony variations (tall or wide, perhaps?)
Combat is a bit more iffy, because there are a few options (though it is my less invested skill since I have officers for that) but maybe offence/defence, bruiser/sniper or some other dichotomy could workbut there are quite a few options as well weightclass of the ship, type or primary armaments
Leadership should be quality or quantity, that is to say better bonuses to officers or less impresive bonueses spread out (alternatively more lower level officers or fewer high level ones)
Tech could let us favor Phase vs Carrier while also adding in flux regulation but I am less certain
One idea is that some skills in the binary option could have a primary/secondary.
Take the idea of industry with trade / scavenging the first skill could give better cargo space and better deals for trade (tariff reduction?) while scavenging could give us more salvage and better fuel efficiency
So what if the better trade skill would net us tarif reductions, more cargo space and a minor fuel efficiency bonus, while the scavenging one could give us more (better?) salvage and fuel efficiency whith a minor bonus in cargo space?
That option could let the player get a bonus on their playstile but still get something from the other side of the aisle that could make up for not picking up one of the binary options.
Take the first Tech skills, one gives us better navigation and the other better sensors, both seem useful and both give nav skills that are useful, so have them both offer that to the player, both skills are given but you either get an emphasis on navigation or an emphasis in Sensors (so instead of forcing you to pick one and tryng to see if you can wrap around to get the other, you can choose your emhpasis while getting a bit of both)
I am still of a mind that some skills shouldn't be binary picks and more be skills to be picked, specially if there is no real viable vs or no reason for a skill to be so up the afinity tree just to maintain the paired approach