Firstly, hi and happy to be a part of the community of starsector ^^
This is my first post and i'm not that good in english because i'm a french native speaker, so be nice with me please ^^'
First things first, i find the Story Point mechanic verry refreshing and full of potential, even more if modders are able to create there own event where you can use them in relation with wath there mod do (I look at you Nerelexin ^^), and since everyone try to find a better name for them, why not Storytelling Point ? It's more accurate (in what you try to do with them) than story point and don't divaricate to much from the core meaning of the base name.
Secondly, after pondering a little, the skills system remind me a lot the one from starcraft 2 heart of the swarm, with Kerrigan able to remap her skill tree after each mission, and in the same game was present an idea that i loved : you unloked a third skill tree after one of the campagn mission. So why not unlock third option skills( one by one, not a full tree in one go) in the skill tree of starsector when the player meet a number of condition, like doing a certain story mission ? The skill in question would be a new specialized skill extending the way you can play, no more powerful, but interresting ( I just let that here, i know that it's a pretty difficult idea to implement but maybe, who know, it will give you other idea Alex ^^)
Thirdly, about perma-hullmod. I love the idea, it give the player a way to put personnality into ship. Yes, some may say that players will always put the most costly mod. I don't think so, because this is a minmaxer way of reflection, and we aren't all minmaxer here. True, there will allways exist people who try to make the most of what they have (sometime, i'm one of them) but it's not the majority of the player (i think). But to continue about perma-hullmod, i've seen a really good idea in the form of specific hullmod who don't exist in stadart version, only in perma-hullmod. That's fantastic, because it give pllayers again another layer of customisation to have a ship with personnality. Moreover, those "legendary" hullmod can be a really good treasure-hunt starter, like synchrotron an pristine nanoforge, with the advantage over those two items that there is more than two of these unique hullmod.
Now about ship in AI fleet who are perma-hull modded. You say that you don't want the player to bypass the use of Story Point to have ship with perma-hullmod, but i really don't see what's the problem here. Those ship are unique ship difficult to acquire. Yes, don't put them commonly, but have them exist in special bounty against pirate of reputation, have them in fleet of the different factions who are known through the sector BECAUSE of the ship and her captain, because this is a good way to put lore and immersion (people talk about them in bar, faction warn you when you're commitioned, a neutral fleet come to talk to you to warn you that THIS fleet is in the sector and that they are returning home because they don't want to die etc...), and it open the path to the player to hunt down and battel those fleet if they want THE ship. Heck, you can even put legendary hullmod on those ship, and make the removable for the cost of a Story Point, to be able to repurpose the unique hullmod on another ship.
Well, it's all i've to say for now. Any chance that you give us a little bit of information about what's going on with the skill and story point system now ? Like how goes the playtest and some of your idea ? (A little bit greedy here ^^') Keep the good work, you're amazing, Alex, you and all the people and modder working for starsector ^^ (And i'm pretty literal and peremptory in my comment but don't take it like that, i respect your work and i know that i'm not the professional here ^^)