A thought on this system. You probably won't like this, but...
What if you just give players their 15 Skill Points right off the bat? De-couple that from Levels; tie Story Points to Levels and Doing Stuff That's Impactful instead?
One of the major problems with the Skills system, in general, that this overhaul doesn't really appear to fix, is that it feels like a pay-wall in the game design, locking away most of the "good" gameplay. Players keep hoarding their Skill Points, comparing builds, etc.- this is all detrimental to the gameplay.
Right now, players are all pushed towards monoculture characters, where they need to be able to fight but also have to be good Colony admins, if they want to "win" the easiest way. I think that having players be pushed into pushing around Carrier fleets optimized via putting as few skills as possible into Combat (and therefore, being unable to explore fighting their own ships much) was one of the unfortunate side-effects of this.
What we want, I think, is to deliberately encourage players to re-spec as they want, try new things out, keep having fun- not feel like they're Doing It Wrong because they invested more than 6 points in Combat (or whatever).
In Vanilla right now, the caps mean that the player's basically unable to go a bunch of routes if they're trying to minmax.
My current solution was drastic- get rid of the level cap and make experience gains considerably faster, so that players aren't nearly so starved. It's not a great solution; you still can't re-spec and eventually even un-capped Levels get slow. But at least the early game doesn't feel artificially hard.
In a system where all players have Skills to allocate immediately, they won't feel crippled or stuck behind a pay-wall. That these Skills are initially weak isn't such a big deal then; there will still be "better" routes, but psychologically, nobody's going to be stuck in Choice Anxiety (at least, not in this area of this game design, lol).
Story Points could then be used to logarithmically improve Skills or unlock Elite, and spending them is good, because they'll give the player something that improves an area a little bit, as well as XP gain to keep moving forward against the endless Level curve.
Story Points could continue to be Level-bound as proposed, but Levels could be capless (but the XP needed to keep going up would, of course, skyrocket). Other Story Points could be gained by Doing Something that scales in challenge with level and times accomplished, keeping it tantalizingly available but not over-powered.
Anyhow, just my $0.02, for what it's worth; I think that, in general, there's a lot to be said for having a system where players respec quite a lot and make themselves into the thing they need over and over as part of a playthrough, rather than feeling that they need to understand <this specific Elite build strat that requires X levels, Y Story Points, and Z grinding>.