Player skills are all over the place. Some are good for your colony, some for your fighters, some your fleet... and aside from the top row all being for your ship there isnt much in the way of a pattern. and your governers have access to a grand total of THREE of your skills, while captains have access to about 10. it frankly feels quite simplistic, kinda feels like you are pigeon holed into a few select skills, and have very little real variety.
so here is my idea. Three separate skill trees for the player; leadership, piloting, and administration. At each level you get one point for each tree and each tree has a couple skills per tier that you can choose between. Instead of using story point to make some select skills elite, add levels to most skills that can be improved by investing more skill points. Splitting up the current 'group' skills would help fill this tree out, as well as offering more customization control to the player, and would make for a lot more room for adding new skills and skill types. while admin/piloting are self evident; the leadership tree would be for fleet/colony wide effects unique to the player. this would make level ups feel a lot more meaningful, your choices too, and wont have players feeling they are neglecting one aspect of play working on another.
Side thought on captains/admins. i see there being two possible ways to make your officers/admins far for interesting too; first give them full access to the 'tree' that is appropriate for them, or by giving them a skill or two that is set and have them gain levels to improve OTHER stats. for example; an officer with fighter support and impact mitigation, and when they level they gain things like '+5% fire rate' or '-10% supplies used'.