I'm a bit confused, because you said that you haven't taken combat skills yet, but you also said the frequent respeccing is due to combat skills, so are you actually doing frequent respecs or not?
Not yet because 1) I do not want to burn through story points like water reassigning skills frequently instead of s-modding my ships and improving my colonies. As a result, I resorted to 2) Ziggurat flagship with Phase Anchor to avoid the need to pick Combat skills because Ziggurat supported by SO Hyperions is strong enough to smash endgame human bounties without any need of Combat skills. (I have five unspent skill points at the moment, the other ten are in Automated Ships and Hull Restoration.) But I can see it will not be enough against a single full Ordos with Radiants and all blue cores, or even if it is for one fight, if I get sucked into a multi-round combat or a second fight too soon, my fleet will die (because my fleet's strongest ships are Ziggurat and Hyperions, and I may get different ships to fix that). I will need to spend my five unspent points somewhere to make my fleet strong enough to defeat full-strength Ordos instead of getting wiped by them. In other words, I deferred my decision on my remaining five skills for later, but "later" is coming up very soon after I resume my game.
Three of the five points will go the Helmsmanship, Combat Endurance, and Impact Mitigation. Helmsmanship because piloting big ships without it feels very sluggish. I want my ships to feel responsive, not slow as molasses. Combat Endurance mainly because if I pilot a small ship, I do not want PPT expiring too soon. Also, if I pilot Ziggurat, I want less time before its CR recovers enough. Impact Mitigation because more maneuverability (great for otherwise slowpokes) and more importantly, Ordos not knocking out my weapons so easily if my ship eats a few hits, not to mention more armor is great for low-tech armor tanks. So that leaves two left for elective Combat skills, or perhaps Wolfpack Tactics and/or Carrier Group for the rest of my fleet.
For Ziggurat, I would want Field Modulation and (if I get enough Omega missiles) Missile Specialization or (if no Omega missiles) Systems Expertise or Wolfpack Tactics (I have many frigates with officers). Ditto if I pick Doom or Paragon for my flagship. However, if I decide I want Onslaught flagship (and Onslaught is very good this release), I want to swap those two skills for Point Defenses and Ballistic Mastery because it turns those HMGs from fringe PD into superior assault weapons. Ditto if I take various ships that work very well with the kinetics and burst PD combo, like Medusa or some of the midline ships. If I want to pilot something with lots of large missiles, especially if it can use Hammer Barrage, I want Missile Specialization.
However, what I have done is reassign skills frequently when testing ships and loadouts in the SIM in preparation for my eventual clash with Ordos, before quitting and reloading the game to restore story points. When I test Onslaught, I had the best results with Point Defense and Ballistic Mastery instead of the other skills I originally planned to take as default general skills because machine guns become medium range. It is like the Lucky's Onslaught build on steroids because HMGs have so much range (and the old Impact Mitigation that gave extra protection against kinetics and/or low damage attacks is gone). If I want I different capital, I probably want Field Modulation for harder shields (or cheap phase upkeep if I take Doom or Ziggurat), and the last skill can either go to Tier 5 combat or Wolfpack Tactics. My Ordos killer fleet is not yet set in stone, but even if I did pick one, I want to change flagship without spending all of my story points to get the right skills.
I do not want to be locked into one flagship for a significant amount of time. Before now, I have picked QoL or generally useful combat skills in the non-Combat tree.
You haven't even clearly defined a problem, so who knows? But the reason the skill point cap isn't 40 is because scarcity drives game play. If you can get everything, then there's no tradeoff. Being unable to get everything you want makes you choose a specific way to play. This is Game Design 101.
Then why did you suggest I mod the game (via altering settings.json or whatever) to raise max level cap to eliminate scarcity in the first place? (Rhetorical, no need to answer.) Not to mention raising level cap does not truly fix the problem of relatively expensive respec when game can encourage respecs if player wants to change flagships often.
I want to play an unmodded game. But parts of the unmodded game are annoying. For this topic, I am venting about the cost of reassigning skills.
There is no such thing as cheating in a single player game.
Hard disagree with that. Even single-player games have rules. Break them and the game has no point. I do not need to waste time playing a game with no rules. I am not opposed to taking advantage of exploits and loopholes that are degenerate but still rules-legal, even if it is a good idea to patch them out.