I think players will get 0-1 specialization skills for each category (combat, tech, leadership, industry). The remaining skills will be the generalist skills which are always the same ones. I don't think this system is worse than what we have now, I think it's better for the reasons you're giving but I don't think it will do much to create variety in character builds. Admittedly it depends a lot on how many skills points we will have and what the actual skills will do.
Let's say it's one specialization per aptitude, and let's say there are 4 "general vs spec" skills in each aptitude, and the player invests into 3 aptitudes. That's 4x4x4x4 possible "builds"; if you end up picking 2 spec skills, the number goes up quite a lot.
The thing is, though, the number of possible builds doesn't matter all that much. What really counts is changes that make enough of a difference to make another playthrough feel significantly different. If there's even only 3 or 4 of those, that's already huge as far as improving replay variety. The current skill system certainly allows for more possible combinations, but the new skill system gives us more
meaningful combinations, as far as actually improving variety goes.
Have you considered a system where skills are organized in rows (representing the skill category) and columns, and a player can never pick more than 2 skills from the same column? I'm assuming 14 level ups here.
Combat: 1 2 3 4 5 6 7
Tech: 1 2 3 4 5 6 7
Leadership: 1 2 3 4 5 6 7
Industry: 1 2 3 4 5 6 7
If balancing all columns against each other is too difficult, then you could make it so that at the first level up, only skills from column 1 could be chosen, at the second level up only skills from column 2, and so on. After 7 levels ups it would start against in column 1. Then you only have to balance skills in each column against each other.
I did consider this, actually! "pick one out of 4" makes the choices harder to balance against each other. Also, since they aptitudes are conceptually different, you'd more often put the player into a position of picking between wildly different skills - i.e. improved combat vs, say, improved salvaging or sensors. Those kinds of choices feel worse, imo, as there's more room for "less fun but more optimal" selections to be made.
Fundamentally, this is changing the structure from "4 tracks with 5 tiers of 2 choices each" to "1 track with X tiers of 4 choices each". (Where in your case X is 7; if it were 10 we'd have 40 skills.) I wouldn't say that's a completely unworkable option or even *that* different from the one I ended up choosing; I just prefer the current setup to this, it was a lot easier to work with.
(Edit: to clarify, I hadn't considered picking 2 out of the 4 skills, iirc.)
Wait so is the designed gameplay to rarely deploy more than 8 ships? Or are you expecting AI ships to fill out the fleet a lot?
"AI ships" - you mean on the player's side, right? I think ideally the majority of the ships you deploy should be the ones with officers. The more ships there are in the fleet, the more busywork there is with loadouts etc; managing around 10ish or so ships like that is what seems about right to me. But the way things are set up you'd have a lot of flexibility about what you want to do. But that's the sweet spot I'd like to aim for.
Also, if the game is balanced around essentially all combat ships having these built in hull mods, it sort of cheapens the decision to put them on. I liked the idea of a big investment to make your flagship special. Instead, I have to allocate a certain number of my story points to keeping my combat ships 'up to par.' It doesn't feel like a decision, more like an obligation.
I'm not sure I understand. If a player can do things to increase their power, then of course the game would be balanced around that? That's... just how it works, right? ("It" being "games in general".)