My problem with Combat skills is everyone has them, and Ordos has the most, but endgame human fleets are no slouches. Also, officers cheat and have access to both Combat capstones at levels 4 and 5. Player needs heavy investment in Combat just to keep up with everyone else if he wants to pilot a ship as strong as theirs, and the player does not have the same access to combat capstones as officers do. No wonder that videos posted lately dump Combat and demote the fleet commander's flagship into a miserable toady or mascot while the rest of his fleet has all the fun.
Back on topic...
My problem with officers is they need to be tailored for the ship, but the mechanics fight this. Officers are treated as NPCs, but in Starsector, this is backwards! Ships are the NPCs not the officers (human or AI core), and officers are the stat bonus accessories for the ship, like jewelry in a typical RPG. (Think of your ships as Transformers, and your flagship is Optimus Prime... or Megatron. Puny humans are mascots.)
Officers are slow to level, and as I play through the game, my fleet and loadouts change, but my officers cannot adapt to an ever-changing fleet. By endgame, I find that I need to fire most if not everyone before I lock-in my final fleet. But there should not be a final fleet just because officers are inflexible and cost too many story points to bring them up to snuff, only for them to be disposed of when they become obsolete after a fleet change. And woe to the player that does fire everyone, for then he needs to spend too much time grinding levels from 1 to 5 or 6 for several new officers and very likely more story points (without refund) to make skills elite.
Retraining should be available at max level (or even earlier if mentored), even if no skill is elite. Currently, player cannot retrain to change behavior until a skill is elite. There is no need for this.
Retraining should be able to change skills, just as it can change behavior and/or which skill is elite. Cost could be one story point per skill changed, and +100% bonus xp per point spent, just like behavior.
Officers should obey the same rules as the player with respect to capstones. They need to get four Combat skills to get one Combat capstone, just like the player, and since they cannot be level 8, they cannot get two capstones. That should at least block 9x missiles on Gryphon. (Then again, if Missile Spec. gets nerfed and Systems Expertise does not change, then Combat should not have any capstones, and all skills could be tier 1.)