First off, I think your post is good feedback. As opinion, as you say, some people are going to disagree, but it is thought provoking, and appreciate the effort that went into it and a number of your points seem quite valid to me. I can agree that some uses are not up to a sufficient standard, with potential for improvement, but I don't think the idea in and of itself is necessarily bad. Execution can vary, but I have seen similar things used successfully elsewhere.
On a conceptual level, I despise story points. In a broader sense, what I hate is arbitrary mechanics. It’d be like if I started an FTL run and had a magical ‘explode enemy ship’ button that I could use X number of times a run. It has nothing to do with the rest of the game, I didn’t in any way earn it, it actively hurts the entire rest of the game and makes me much less engaged, and it doesn’t even have any thematic or mechanical engagement with the game besides, essentially, lowering the level of thought required to play it.
Personally I don't see story points being any more arbitrary than an experience bar and skill trees. I would also argue that in the case of story points, you did earn them, in the same way that you earned skill points and progression down skill trees. Certainly there were enough posts stating there were not enough of them that Alex hot fixed an increase to the gain rate post level 15. What the appropriate rate of earning is certainly up for debate and likely going to depend on personal preference.
However, to say you don't earn them, is like saying you don't earn credits in the game either. By definition, story points have something to do with the rest of the game, you can't get them without actually doing something significant in game that gets you experience points. Arguably, credits are earned easier than story points - you can get those by simply sitting in your ship orbiting a planet, with a commission or for the first few cycles of the game.
I've seen similar concepts done in a number of other pen and paper games, like fate points in Fate, or hero points in Pathfinder, or force points in Starwars D20. The later two examples are explicitly refreshed by leveling, although doing cool stuff in story can also have them be awarded by the GM. Kind of like how the story line in Starsector hands out story points in a few places. Fate points in Fate let you occasionally declare things about the situation at hand, briefly pulling overall narrative control into the hands of the player instead of the game master.
They're all arbitrary in a sense, but do provide a limited resource that lets you go above and beyond on occasion, breaking the rest of the normal rules, and thus letting the characters feel more special and unique because they're breaking the rules the NPCs can't. Simply because they're the main characters of the story taking place.
I want to be clear that I'm not criticizing the various systems and mechanics that are accessible via story points; I hate the points themselves. In every instance in which they are found within the game right now, story points do one of three things; devalue an existing mechanic or system, circumvent the same, or directly harm the game's foundations.
Experience is perhaps the ripest target, but at least that gives me a sense that I’m growing and becoming more adept. It is, ironically, a far better way to make me invested in my character than story points are.
How do you see story points as a difference from skill points, a limited resource generated by the gain of experience, and spent to devalue existing mechanics (industry tree fuel logistics for example) or circumvent mechanics (transverse jump in the tech tree circumvents a large amount of potential encounters on the campaign map, and makes smuggling or escape in systems trivial in many cases)? "Directly harming the game foundations" is a bit more of a nebulous term to me, I'll admit.
Story points, however... The easiest way for me to sum them up is to compare them to cheat codes. The kinds I used to abuse a decade or so ago when I began playing computer games. I can distinctly remember the day I realized how much I was cheating myself by using them to circumvent the game, the challenges, the fun presented to me. Story points leave me with that same awful, hollow feeling; and in many cases, the way they're used is barely a step removed from a console command, or in the case of SP disengage, literally equivalent to a console command.
That strikes me as a question of overall difficulty then. I can use "cheat codes" (i.e. modify game files) to make the game harder as well. Many mods and the game itself can be tuned to one's desired difficulty level. Many, many people use the save and reload functionality, and I do as well depending on my desires for how I'm playing the game at the time. Some uses of story points mitigate the potential losses a human being can cause through mistakes (being inattentive, literal misclicking F instead of D while piloting an Onslaught, etc), which I prefer to save and reloading. Having played through an iron man respawn or two, respawning is not always the best use of my time. However, I feel risking something and failing forward, is overall better gameplay instead of reloading the exact same fight 3 times, and story points at least in theory can help facilitate that, as another resource you can lose instead of your entire fleet. Yes, they do make the game easier, but so do skills, credits, commissions, and a host of other things you can earn by playing the game.
If the game is balanced with them in mind, then I can't see it as a cheat code, it's an resource you're expected to use. Currently, I'm pretty sure you're expected to spend story points on hull mods for a number of your ships to be able to handle end game triple Radiant fleets or the <new redacted> end game bounty with a classic fleet composition (as opposed to say, Derelict Contingent or Phase Mastery/Systems Expertise solo chain Doom). Whether the game is currently balanced and at the correct level of difficulty with them is a different question, but in principle, it should be possible. Rate of gain is a large part of tweaking that.
But I'll get to that in a moment. These things do not make me feel like I’m writing my own story, or that my character is having moments of brilliance, or that I’ve in any way earned something.
This is fair. I have used story points on some of the non-violent story line options, but there's no real way to change the overall story line. On the other hand, branching story lines in computer games are a gigantic pain and take massive amounts of effort relative to the payoff players get from it. As for feeling having earned it, that I still feel is related to the number you have on hand. If players received 1 story point per level, and 1 per 4 million XP after 15, I'd bet spending a story point would feel far more earned.
I do feel building in hull mods with story points is basically saying "This ship is important to me". For most players, I'm willing to bet they don't double or triple s-mod every ship they get their hands on throughout a run. Again, rate of gain can adjust how significant that particular feeling is to me.
There's not even a reason to call them story points. Again, they have a connection to the game about as solid as frog snot; you could call them magical genie lamps and it would be just as appropriate, and in fact would probably be more appropriate given the way they're used. And no, not Robin Williams genie. Will Smith genie.
I could see them as luck points perhaps, in the case of guaranteeing recovering a derelict or escaping without a fight. Although improvements to industries and ship hull mod integration strike me as not lucky. Main character points, or single player game points perhaps.
At the end of the day, these are a resource which not intended to scale exponentially with stage of the game like credits or ships, but are more of a slow but steady gain (at least past the first 6 or 7 levels) for actually doing things which earn you XP. Past a certain point, credits become meaningless, you have access to all the ships you could possibly want, which would trivialize certain problems. Who cares if your fleet blows up when you can replace the whole thing from what I've got sitting in storage and constantly producing more. Bribes for the Hegemony? Sure, I've got tens of millions.
It's a completely different feeling when you have 30 or 45 story points invested in your fleet at end game in 0.9.5a than end game in 0.9.1a, where all ships were interchangeable. It becomes much more of an investment than merely the ships. That is likely hours of effort poured into the fleet that you can't simply replace at the drop of hat. Or spending a story point on bribing the Hegemony feels far more costly than spending a million credits. That right there does feel like a story change, as that's literally preventing a war with Hegemony solely through you ability to fast talk or charm the inspectors, which by rights should is an incredible feat of persuasion. I mean, the alpha core can't seem to convince the Hegemony to stay away and save themselves, so how does a mere mortal as yourself do so?
As noted at the beginning, I agree not all options are good enough at this point. There's room for improvement, but I don't think it's necessarily the wrong direction. As noted by others, I feel the campaign version of Starsector (as opposed to missions selected from the main menu) is closer to a pen and paper RPG in progression than a rogue-like FTL or Hades. A campaign is intended to be much larger investment, and thus it should be really, really hard to reach a respawn condition, as it's potentially hours of progression lost. Losing something valuable, but less than the sum total of the run is a much better balance point in a game like this, in the same way that spending a hero point is much better option than a random string of critical hits dictating a Pathfinder character died in some meaningless side encounter. It's a real cost, but its not the whole game, and making you reach for the reload button.