Won't this have strange effects in AI fleets?
Nope, checked that. Officers do not apply fleetwide bonuses to their fleets even if they know them.
If the ai admiral char has some, those will apply, and that's fine.
Since many skills are slightly weaker to compensate ai officers will also be slightly weaker, but so will your own. if you'd prefer this mod to be entirely additive (just makes skills better) let me know but right now I prefer this.
If you make it 3 points an aptitude level, and you start with 1 point in every aptitude, then it takes 1 fewer total skill points to get level 1 in a given skill, exactly as many to get level 2, and 1 more to get level 3. Plus now instead of wasting points in aptitudes, you've got (0,2,4) points in other skills, ones you would probably have gotten anyway. So it doesn't really matter if the first level skills aren't worth taking, you come out ahead unless you really wanted only that one level 3 skill
I'm going with 4 pts per aptitude, but yes not wasting points on aptitudes is intentional. This way lets you spread out or specialize but NOT cherry pick