Don't mind if I answer for OP. Hoarding SP for "value" usage isn't fun compared to using them incidentally for plot purposes. Besides, fleet build isn't something that should be gated by how much SP you can grind imho.
Instead hull mods could gain xp, the more you use a ship the quicker its hullmods level.
the xp increase the effect of the hullmod, a bit.
I'd hazard a guess that the OP is opposed to grinding SP since they're just swapping it to a ship specific XP grind from a generic player XP grind (which in general will make the grind longer since you'll finish the grind based on when you acquire your very last ship for your fleet build).
Hoarding will likely happen for some players anyways, since as you remove uses for story points, the number available will need to shrink to make their uses meaningful. If story points are not limiting your decision making in some way, they should just be removed as they are not actually doing anything but making you click more.
elite-skills:
they just feel like a remainder of the old 3-tier skills for officers.
Drop them.
Given the stated reasons by Alex for including elite skills (giving the player an edge over the average run of the mill NPC officers, as well as making Remnants even more terrifying than normal fleets), what would your new solution be to handle those issues? For example, other than Radiants, Remnant ships are nothing to write home about, and without their alpha core fully elite officers would be significantly weaker, on par with many officered faction fleet ships. Similarly, a 5-6 combat skill investment player character would have the same bonuses as any level 5 or 6 officer, where as with the current system they have an edge with 4 more elite skills.
Is this a desired result, and if so, why?
colony upgrades:
use Credits instead and may be an industry xp system.
And remove the exponential cost scaling, because an exponential cost can only be overcome by an exponential growth.
If you're going this route, why not just remove the story point use instead of replacing it with credits and another stage of building, and just increase the time for things to build and costs associated? Even more staged building than what we have is not that interesting to me. If you're expected to do it anyways (because credits become effectively unlimited in the late colony game), just remove the extra clicking rather than making me do more busy work. In this proposed system, since the expectation is you upgrade everything to the max level with credits, the lower stage profits would be reduced, so the final expected state is the same as now (which is colonies with 1 or maybe 2 story point upgrades).
Right now, story points are increasing with every application to a colony because the expectation is that every industry should NOT be fully upgraded with story points. Exponentially increasing costs are by definition a soft cap mechanism and achieve much of the same effect as a hard cap for most players (I would hope). I'm pretty sure it is intended to make you stop a one or two uses to shore up places on your colony where the RNG was unkind in terms of resources or colony items, not give you a reason to grind for 10 years in game. If the soft cap is failing in communicating that intention, then maybe Alex needs to convert it to an explicit hard cap, say no more than 2 industries can have story points applied per colony.
As it stands now, with story points being usable on ships, officers, skills, colonies, and dialog interactions, and in a somewhat limited quantity, you are telling the game what is most important to you. If you're spending 70 story points on your colonies, you're making a statement about how you want the greatest star empire ever. If you're spending story points on officers and ships, you're saying you want the strongest fleet. If you're spending on personal combat skills and dialogs, you're saying your personal character is hyper competent. These are the kind of overall choices and changes in the game play that story points were introduced to try and foster. If you're just spending credits on colonies, and ships, officers, and skills don't use story points, then story points are much more limited in scope in telling the game what you actually care about, and are much reduced in changing how the game feels from player to player, run to run.
Perhaps the current story point implementation doesn't work for some, or perhaps the majority, of players, and the fact you can grind for years to eventually get as many story points as you want blunts the effect, but I can at least see what Alex was trying to do with the system. I feel like a number of suggestions take the narrow view and keep looking at the various uses in isolation, and want to replace it with different progression mechanics so that you can raise everything to the maximum simultaneously, but I fear doing so loses the larger idea that Alex was going for.