I very much dislike current SP system in general for the exact reason a poster in this thread mentioned: they are essentially just an extension to XP system and, because you can obtain endless XP (by farming), they are, eventually, an unlimited resource that's used for both consumable options AND stuff that's supposed to be permanent. The payment for them is your time.
But let's go through different stages of the game.
Early game:
In early game, SP are extremely precious because you are both unable to get a lot of them quickly and there are limited opportunities to get them too. This makes using them for most "consumable" options feel like a complete waste, but s-mods are also weirdly off-putting to get because losses should be expected at this stage and it is not unlikely you might lose your first s-modded ships. So, in early game SP fails because there's this desire to conserve them and only use them on genuinely permanent stuff -- elite skills possibly, maybe even improving early colonies if you're that person.
Mid game:
In between early game and mid game, there is a period in which things feel balanced, but it is short-lived and it ends once you acquire a decent fleet because suddenly you are at a point at which you become able to obtain a ton of XP and, by extension, SP, getting so many points that you won't know what to do with. It is very likely that at this point you will start investing into elite skills fully and could even consider using SP for consumable options. Officer training also possible.
Suddenly, SP are very abundant and you have many venues to spend them on, until you run out.
Late game:
By now you are level 15 and any further SP you get will be obtained naturally and in considerable quantities. So now, there are two scenarios. Either you have no SP and just have to grind for them or you have too many once again. By this point, SP is mostly spent on either experimenting with s-mods in sim [though I'd rather just savescum, this is just bad design imo], respeccing skills and consumable options.
The Problem:
So, what do we have? There's almost no period in which consumable options besides special maneuvers would warrant some deep consideration on whether to use an SP or not because there are almost no circumstances in which using an SP is not binary. The way the game progresses somewhat follows a sigmoid curve and SP generation generally follows suit.
Most story or quest-related options are just clearly better to use an SP on and unless you run the (story) missions in exactly the right time-frame with the right progression, you will either always use an SP or pretty much never depending on which side of the sigmoid curve you're on.
For instance, negotiating a higher pay for a delivery mission, getting a smaller loan interest rate, convincing the beta core to surrender etc.
Then we have things like s-mods and officers. The way s-mods are right now, I strongly disagree with the poster that mentioned that s-mods are giving identity to ships. No, they don't, because SP are infinite so in principle you will always be able to scuttle a ship, get a new one and install new s-mods there. You are paying in your time and credits [which, with colonies, is also just your time]. S-mods are not truly permanent in this sense with the notable exception of Mr. Z with a weird workaround even there.
We also have officers that do in fact get truly permanent SP options in that you may not change the skillset of an officer afterwards no matter what, but you can dismiss the officer, get a new one and just mentor them from scratch, so even this is not really permanent on a global level, though you might get attached to particular officers for roleplay or immersion reasons.
So, given these two considerations, why are we pretending that s-mods, player skills, officer skills etc are (semi-)permanent? Everything here is very much mutable. And the reason? SP are infinite, you buy them with your time wasted farming (in worst case) or naturally by fighting stuff (in best case).
And thus...
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.
tl;dr
Make SP part of player's LVL and make s-mods, skills and officers all use SP from that shared pool, so the player has to carefully assign SP out to specific things depending on their intent, but otherwise make it very fluid to shift from one doctrine to another once you get the levels. In other words, make SP act like a secondary flat skill system and call SP something like fleet skill points to distinguish from player's personal skill points. Use different resources or make free repeatable options that don't have an impact of indeterminate duration on player if they are not cancelable as well.
TT's colony crisis deal is a good example of a place that should take a bite out of fleet skill points from the player given the deal is otherwise permanent and beneficial yet can be cancelled.
Note of lvls:
One of the bigger issues in the game for me is that the progression is a sigmoid curve in lvls as well. Some different thresholds should definitely be set to make it more linear.