I think this would only be a problem in a competitive mutiplayer game or an extremely hard game. It's OK if skills are unbalanced as long as the weaker ones still allow you to overcome the challenges the game provides, which is the case. You can even succeed without any skills at all. I think the main function of skills is to provide a varied gameplay experience from run to run and to allow for roleplaying.
It is a competitive game... against NPCs, and max level NPC fleet commanders have a skill advantage, no dead aptitude tax, 21 in personal skills, and for fleet commander, (maybe) up to 15 for fleetwide skills. This is more than the 33 points players get (42 minus 9). Even mere officers are doing well. Effective 30 points (21 points and no aptitude tax for a 9 point discount), they are only up to four skills less than you or NPC fleet commander (who gets some among Officer Management, Coordinated Maneuvers, Fleet Logistics, Fighter Doctrine, and Electronic Warfare.)
Why spend three points leveling up one pilot-only skill when I can spend one in Officer Management and get two officers with (up to) 21 skill points (or 7 max skills) each?
My character is the only one who can take fleet or campaign skills. My officers can only take pilot-only skills. It is like officers are telling player
"We need a healbot for our balanced party, and only you can do it, so you take those support skills and like it while we take all of the combat glory, har har! You dare not weaken our fleet by trying to become one of us, slave!"Yes, I can make due with no skills, but being stuck with a stock ship while NPC officers get overtuned ships is no fun. However, if I try to match NPCs, I probably end up gimping the fleet due to lack of points.
My point is if you try to match NPCs in skills spent, you have none left for anything else. No Loadout Design 3, no Navigation, nothing in Industry. This is not mentioning that 21 points dedicated to pilot-only skills is not enough to get all such skills. Officers cannot get everything. There are more than enough pilot-only skills that you cannot get them all even if you sink everything into as many as you can.
And we will get more skills for colonies, but maybe no more skill points. We are already squeezed enough, and it will only get worse if we get no relief.
Isn't it kind of a good thing if skills are good enough that you *want* them all but can't do everything at the same time? Doesn't that lead to meaningful build variety, and replayability?
Not really, especially if NPCs have more skills than you. Or that NPCs have nearly or as many skills as you, but they can only take the fun personal stuff while you are forced to take fleetwide or campaign stuff to make everyone better, and if you try to emulate your fellow officers, you gimp your fleet because you do not have enough skill points to branch out a little.
You are strongly pushed toward "non-combat" admiral, if you want to have the strongest fleet. If you try to be as competent as a max level officer, you spend all of your skill points doing so and have nothing left... and probably gimp your fleet because you had the audacity to get to their level and have no points left to get the fleetwide/campaign/exploration skills.
P.S. You can fire officers and train replacements if you do not need their skills anymore. You cannot fire yourself (short of a starting a new game). Want to be the best Astral pilot? You get all of the carriers skills. What, you tired of playing carrier and want to pilot Paragon now? Sorry, you have useless skills, you will like being a carrier pilot for the rest of your game. You should have taken general-purpose skills for yourself and trained an officer for the job of piloting a carrier instead.