I think the bigger issue with Story Points is that there's only two groups of uses for them: Those that benefit and strengthen the player (S-mods, officers) and those that are useless and have no real benefit (fluffy dialogue, arguing for better pay, the sword duel). One is not equal to the other and their value is not at all comparable. As there's no "speech skill" or anything to fill in for the latter we're stuck paying valuable green points, which just means nobody picks those options, or they pick those options to see the dialogue and reload a save. For example, in extraction missions you could spend a point and a sum of credits to bypass going in with marines. It's a green point tax and it makes a worthwhile consideration into a blindingly obvious choice as it's far, FAR, cheaper to buy the marines the mission giver tells you and just raid and eat a few points of reputation. If there was a choice between saturation bombing and genocide, or paying premium currency to avoid it, I think the average player would choose the former.
There is a value to Story Points from a development perspective. It's very easy to slap it on for optimal choices and the story/quests can be written with the player having points in mind, pick the cool option and just let your imagination do the details. The problem is that this is shallow from a player perspective and they're inconsistent. Everything uses these points and they have no tangible basis in the game. For all intents and purposes it's pulling a genie out to do a magic trick. Need to escape a fight? Divine intervention. Want to haggle for better pay? Divine intervention. Want to intimidate someone away? Divine intervention. Want to colonize a planet in a declining sector? Oh you can just do that normally with bulk commodities.
Honestly they're bandaid solutions for gameplay problems. If officers need mentoring because they level at a glacial pace without it, maybe the problem is that they take too much XP to level up. If a ship is difficult to make work without specific meta builds or S-mods (or both) then maybe the issue is that the ship needs some help in stats. If you get hit with an unavoidable and unbeatable fleet in hyperspace you better have that genie on hand because fighting a retreat battle might as well be suicide with how incredibly difficult it is to escape with even a fraction of your fleet.
Not to say we should nix the whole system as the development has already been put in and there is merit to "plot armor" if we lean into the space RPG side of things, but as it's the only option to do things it could be a lot better.
The Solution:
I believe SP should no longer be tied to XP, but to player's own level. Player's max level (without using mods) is fixed to 15 and I believe the player should be given a certain budget of SP that are then used for intended-to-be permanent options, but the player should be free to do everything that currently needs SP as long as they are within the budget.
In other words, s-mods become like ship-specific skills [in the form of OP-free hullmods], dare I even say skill-mods. Player's level already limits how many skills they can have. Not only that, but they might even be a shared pool: more s-mods on the ships in the fleet -> fewer elite skills for the player. This ties in nicely with existing ship limits too.
Ditto for officers: perhaps officers should still be able to level up, but the player can immediately temporarily assign them with target skills and be able to freely change or change for a nominal fee their personality and make skills elite. As officers level up, the player gets refunded the fleet skill point that they can use elsewhere.
Ditto for certain special events such as colony crisis resolutions that provide you with a permanent benefit. Kanta's favor might be one of those cases where assigning an SP to keep pirates off your colonies might work out nicely, but you can still pull out and lose the protection, but with an option to resolve it via non-SP means.
Naturally, this implies that the player should be freely capable of respeccing their skills and even changing out s-mods [whether directly allowing to remove and add s-mods or by having to scuttle and getting a new ship, but this still refunds the fleet skill point back, so no extra time lost].
All of these apply to cases which provide a benefit that will last forever until the player cancels it. S-mods, officer skills, special events, maybe even certain story missions.
Now, the question of consumable options remains. In my opinion, the vast majority of options that are taking SP now should just be freely available or available through a resource that's not paid for in player's dedicated time. This includes pretty much all story-related choices along with a few bar mission ones. The delivery mission, the blueprint-for-SP mission, you name it.
Only common two remain: special maneuvers and limited repairs.
And in my opinion, these can be very easily paid for in fuel and supplies respectively. The "special" maneuvers might involve detonating fuel or something to orion outta there. Given that many unwanted encounters occur while exploring, this poses a considerable danger for the player that chooses to do so because the fuel cost of this maneuver should not be static and they should feasibly risk getting stranded by doing so, not to mention having to deal with repairing the ships afterwards, both from harassing fleets and from the fallout of the explosions.
And limited repairs using many supplies would just make sense and have much the same intent as disengaging.
As far as complete reworks go I agree, you have a point to put in yourself with skills, and a point that's of more surgical use in more—but still significant—applications. It'll take getting used to not triple modding every ship in my fleet, but we used to just not have them in the first place and relied on making ships good without green crutches. It would make them a lot more special and place more value on choices as each is significantly more meaningful with a finite number to pick. Special Maneuvers just highlights the issue with retreat battles and how incredibly punishing losing is as ships and any rare cargo is gone for good. You'll always take a supply, fuel, and CR loss over the guarantee of losing nearly everything. Even engaging head on has less risks than a full retreat because there's the opportunity to wear out their fleet just enough to run with your logistics intact. For that I have no idea how to fix without also making it frustratingly difficult or tedious to hunt down fleeing NPC ships. You can't bribe pirates off with money or cargo either, only fight to the death which just begs the question on why we can open comms with them in the first place.
While Story Points are infinite, they come at the cost of your time and after hitting max level this generally means grinding Ordos with huge XP multipliers. You're guaranteed 60 just by leveling up to 15. That's 20 ships with 3 S-mods a piece. Officers are also hungry for them, 5 per officer if you mentor and max elite skills which is 50 points for a full crew of 10. It's expensive and you're not likely going to invest in all that, but it shows those are by far your largest SP sinks. But that depends on the person on where their priorities for benefit lie, IIRC Megas saves most Story Points for colony improvements as it's n^2 costs stack up quick. The way Story Points are balanced is by bonus XP, nice in theory but there's not much difference between 0% and 200% simply because a smart player is always going to have bonus XP, and liberal use of it means there's always going to be a green bar there until you hit max level.
Compromise:FTL has a great solution for these in the form of blue options. You don't need to add 50 different special gizmos and "minefield" consumables for each different case, we already have them in the form of skills, ships, and common commodities. Let SPs be valuable and not waste them on fluffy dialogue and minor benefits, instead let having certain skills and ships or hullmods do the talking and qualify you for being able to do these cool things, see the special dialogue, and roll with it without feeling like you just kneecapped yourself because you could've mentored an officer with that point, or built an S-mod, or made a skill elite, or escape a fight that would've resulted in a fleet wipe.
You don't need concrete rules, just close enough to be plausible.
A combat capstone lets you choose the "I studied the blade" option as you've invested into combat skills. Let the player haggle for higher pay if they've got a leadership capstone as they've got a handle on working with people and negotiating contracts. If the player has Electronic Warfare and Automated Ships they can use this expertise when dealing with AI in place of SPs like the Beta Core. Having industry capstones can let the player pull noticeably more ships from the "difficult recovery" pool. With Officer Management and Training you can bluff to the Diktat officer on Volturn's shrine. With XIV ships you can fast talk a Hegemony patrol officer into thinking you're someone important, same with other faction specific ships and maybe pay a small rep cost later. With an Ox and a technology capstone you could possibly perform "special maneuvers" to escape from a fight, maybe at the cost of D-mods because you burnt out its drive field stabilizer and throw in costs of fuel and machinery as well.
Sure these most of these aren't consumable payments, but why not reward a player for the finite skill point investment or their choice in ships? Let them feel good they chose to invest in X or bring along Y and Z. If you need to pay something, let them pay with supplies, fuel, crew, and heavy machinery; things that every player is guaranteed to have. And if all else fails you still have Story Points for when you have nothing else to give, the system is already in place so it can still see use.
Story Points can pretty much be replaced with gameplay. Problem solutions found and done through gameplay will always be better and more satisfying because it's both grounded in the setting's rules and rewards the player for choosing the things that enable them. The fact you can build in hullmods and make a better Onslaught than the XIV version (which is lost pre-collapse technology) out in space with no need for heavy industry or domain tech is silly. Let Story Points be valuable as backups for real qualifications or as limited payment for real substantial bonuses to player power, and don't let their existence get in the way of the player seeing cool or slightly more optimal choices. The simple fact of the matter is they wont see these things because the option never justifies the value of the point spent. There is no reason to spend a Story Point if the difference is a few thousand credits.
