No, the premise is backward.
The skill system discourages frequent respec. That's why it costs a story point to do so.
And that is a problem because it is too much grinding to fix mistakes or even just to have variety in playstyle if I quickly bore of my current one, and fixing mistakes is story points robbed from fueling s-mods for more ships and to satisfy the absurd and asinine 2^n costs of improving multiple colonies. Story points is the Starsector name of Vespene Gas - currency to be spent on upgrading your faction assets.
The game encourages respec because flagships and fleets want different skills to be the best they can be. It is not as bad as the previous 0.95a releases with the mutually exclusive xor skill system, but it is still there. However, the current respec cost hurts if someone wants to change his flagship and/or fleet frequently but does not because he wants to save up story points to spend them on more important things. So, yes, the game also discourages respec at the same time.
Having mechanics that both encourage and discourage respec at the same time does not feel good.
I don't see it as a problem that the player needs to spend a story point to respec. It means "something", but is not an onerous cost. A story point is fairly cheap. At the early levels, you get a lot of them quickly. After level 15, when you can hit Ordos fleets, you should be getting roughly say 1 to 4 story points per Ordos fleet (assuming your XP bar is in the green). If you can't tackle Ordos fleets yet, then you obviously get less from faction fleets, but they're also correspondingly easier. If you would rather put the story points into s-mods or whatever, well, then that's on you. If you're already at the point of wanting to min-max the game by doing lots of respecs to keep your flagship optimized while changing flagships frequently, then spending the 5 minutes it takes to kill an Ordos fleet shouldn't be a problem.
My fleet has been at max level for a long time, so early game is irrelevant. I do not have an Ordos smasher fleet (yet) and my current fleet will wipe against double Ordos and likely struggle against full Ordos with all blue cores. I fought weaker Ordos on par with or mildly stronger than endgame human bounties (and the rare double human bounties) and identified critical weaknesses in my fleet. The only way I can fix that is to spend my five skill points to optimize my flagship and fleet (and probably fire most of my officers and train new ones - more tedious grinding), but doing so will lock in my fleet in an unsatisfying way. (For example, getting skills for Onslaught flagship, but later, I want to pilot Ziggurat who does not need PD, or Paragon who does not need Ballistic Mastery, or Legion XIV who wants Missile Specialization to spam those missiles, or Doom who wants Systems Expertise to abuse Mine Strike but has little use for Missile Specialization.)
Skill point without refund, or even with refund with current slow bonus xp gain at max level, merely for metagame QoL (of changing your party members and reequipping the party skills), is an onerous cost.
To advise OP to add more skill points or story points is no different from saying have no respec mechanic and to just edit your save if you want to. Its not a good solution.
Totally agreed. If I can "fix" the problem by altering the game (outside of in-game settings), I would not post the topic in the first place.
Starsector is too long a game to replay over and over again from the beginning. If anything, it is an level and item grind much like Diablo II that encourages long term play of a single character, or at least a dedicated magic find character and a munchkin recipient character (and player probably wants several recipients). But with how slow gaining story points are without an Ordos smasher fleet that can slaughter Ordos fleet for +500% xp, respecs that cost story point when player can swap flagships freely cost too much (takes too long to grind up another story point with fights that grant less than +100% xp). Also, having the perfect Ordos smasher is effectively winning the game, unless the goal is to colonize the whole sector and wipe out the core worlds in the process. (I do not have time now to grind for full sector colonization.)