Megas is, as usual, largely on the money with his assessment.
Some of the problems with the skill system at the moment are:
1) Many skills have 'dead' levels - where the bonuses are insignificant or insulting, particularly based on build - which combined with aptitudes often feels punishing. Putting your one skill point a level into getting something later feels mediocre.
2) Certain skills are standouts and feel absolutely mandatory regardless of build. Looking at you, 10% OP. I'm not even sure what the first two ranks of that skill line give, from memory, and I don't care. They could be blank, and it'd still be one of the best skills in the game. Others just feel mediocre. I understand the logic behind say reduced HE damage to shields, it's just completely worthless and nobody cares. Or about increased damage to, what was it, fighters and missiles? Others still feel like taxes - oh, you didn't take ECM? Enjoy your range penalty.
3) 'Group Buff' skills often are on the same level as or otherwise outclass 'Solo Combat' skills. This was particularly noticeable in earlier versions where there was a carrier command that affected all fighters in your fleet, and one that just affected your own. Even now - would you like 25% increased CR for your ship or, for, uh... everyone's... ship?
4) Taking all combat skills doesn't particularly make you feel great, especially given most AI officers can just do the same thing. It doesn't feel rewarding, especially when they get those skill ranks easier than you in a sense, and it feels punishing in that you're deliberately giving up 'command' buffs (which are by and large superior mathematically with even a small fleet, and outrageously better with a large one compared to the often similarish combat bonuses) to do so - you're the only one who can take those, but any pilot in your fleet can take combat skills... taking them just puts you on their level, it doesn't make you feel strong.
I've seen ideas of allowing the player to pilot their own officers ships with their bonuses, or being able to recruit fleet leaders, but I don't think those are the best approach. What I'd recommend is giving all flagship commanders - the player, as well as the leaders of any opponent fleets they encounter - their own, separate buffed up variant of combat that is superior to the regular officer combat tree.
This means rather than feeling like you have to choose between very powerful fleetwide buffs that are mathematically superior, or being actually as compotent in combat as your fleet officers (but not much more), you can instead pick between reasonably okayish with very good officers (high leadership boosts - which also affect you), as competent or slightly more with a buffed fleet (mixing between them), or by being an absolute combat monster and mostly eschewing leadership skills (all combat). You don't feel like you're giving up something unique only you can have (leadership buffs, in a sense) to just be... on par.
In addition, it means you'll be likely to face the occasional 'supership', lead by an high level flagship opponent who took combat skills instead of leadership skills.
The real biggest problem with the system is the perception that you're suffering taxes, that you're being punished by taking the optimal approach (leadership) by being worse than your officers, and that even if you do spec into the mathematically inferior combat tree, you don't really feel as rewarded as you do in the old days where it really made you a combat monster. Buffing leadership was necessary, but I feel that combat - particularly for the player - needs some changes and buffs, as well as making the player feel more unique rather than that they're giving up extremely good fleetwide bonuses to be... on the same level as the AI.
I know I exaggerate a little here, but we're talking perception, and I know I'm not alone in feeling this way. Maxing combat should make you feel powerful, not like you're paying a tax.
It'd be nice to see the 'lone wolf' style of the old days a little more playable than it is currently, too. I know it's not really the design intent, but it was absolutely one of the most enjoyable ways to play for me and I really do miss it.