Wanted to briefly say that I'm thrilled this mod exists. I've fantasized about a similar system in the past, but never bother to attempt it. This definitely fulfills the dream.
I've only played with it for a few hours now, but I'd like to provide a few bits of feedback.
1. Echoing what has already been said, I do agree with the sentiment that some aptitudes are too laser-focused on certain areas ("Support," "Small Craft," and "Automation," as you've stated). Sounds like from your earlier response that you're considering some ways to address this, and I think that's the right move. I'm unopposed to the concept of a specific playstyle each having an "optimal" aptitude for players who want to go all-in on something (carriers only, mass frigates, automated ships, etc), but I don't think said aptitudes should horde all of the relevant skills. Spreading things out a *bit* more would probably foster some more interesting builds and prevent situations where players lock themselves into a specific set of XOs for the whole run.
2. I'm concerned about the aptitudes with skills that that modify hard limits: s-mod count, officer limit, flux caps/vents, etc. These were fine(ish) when they were attached to the player: speaking for myself, I'd never even reassign/swap those skills as they were not only powerful, but also a hassle to change. SiC seems to be a lot more accommodating to the idea of swapping skills/XOs more regularly than a player would reassign their skills in vanilla (which is a great concept). So, if I pick a skill for an XO that allows +1 s-mod -- yes, that skill is fantastic, but now it's also a pain to remove that XO because, after enough time, I've probably built my whole fleet around that one skill.
Personally, I'd prefer any skills that adjust hard limits to exist on the player's skill tree rather than an XO's. Or, maybe a hot take: those limit-adjusting skills can just be removed entirely. 3 s-mods per ship is insanely good. With the power that 3 leveled-up XOs give to a fleet, more s-mods just isn't needed. Though, I'd still like some way to field up to ~10 officers... if it were me, I'd probably just set the limit at 10 and call it a day. Officers are just too good and interesting mechanics-wise for me to not immediately choose to go all-in on them.
Thanks for all your work in creating this; SiC is a huge breath of fresh air. While I appreciate and respect all the effort that Alex has put into the vanilla skill system, no iteration of the base game's approach has really "clicked" for me as well as SiC has. I may toss some more thoughts your way as I go through my current playthrough.