Hm.
...You know, if I were trying to balance this skill, I might take a page out of Interstellar Imperium's book, and just have the skill description say "Improves ship systems, typically by reducing cooldowns or improving regeneration rates", and then have each individual ship system be responsible for determining what the actual effect is.
And then you could have, say, things like "Improved Fortress Shields: Halves the system activation time, triples shield unfold rate while active" that would just not make sense as bonuses to any other ship system.
I like II's upgrades, but one thing of critical importance is that those system upgrades take place as just one component of an entire package that changes the base hull's play style. That's the main reason why the package enhancements are as interesting and work as well as they do.
I'm not fond of stretching that idea to System Expertise though, which is more intended as a general buff to ship systems in a game where very few things otherwise enhance them. The way it currently does things is fairly universal and applies to most mod systems as well; only a few very-specific systems (certain toggle-based systems such as Fortress Shields) receive absolutely no benefits from it, and even that specific case can be solved with a "generic" buff.
Plus, the way the current system enhancement implementation is done right now, one can make additional ways to generally buff ship systems, such as through a hullmod or a ship system that bestows similar benefits to allied ships within range (or conversely: impedes the performance of systems of hostile ships caught within range)
Only thing System Expertise needs is the precise numbers on certain attributes checked (namely +50% range and charge rate) and the introduction of a parameter which reduces flux use on ship systems that have them, to make it a bit more universal.