I'm getting the strong feeling that there should be a minimum on the scaling skills. Bulk Transport is a good example here. +50% Cargo Capacity divided by current cargo capacity divided by 2000 is not a bonus that scales with the size of your fleet, it's a flat +1000 cargo capacity if you meet the minimum requirement of 2000 base cargo capacity. If you're a big transport fleet with 20000 cargo capacity, you don't care about this skill, it's +5%. If you're a big-time trader that wants to carry a lot of cargo, spending your level-up on the skill that lets you carry more cargo is not very helpful.
I like that the skills scale with fleet size - or more precisely, I like that they mean a small, elite force is more elite than a big, fat fleet. I like that I can take Weapon Drills, and if I'm a little fleet, I get a big bonus. But they need to not scale into nothing. Currently, that skill would give me +2%. It's a joke.
More specifically, what I want is for the bonuses to be upped a bit, maybe 20-50% (so Weapon Drills would cap at +12-15% fleet damage) and have a minimum of around one-half to one-third of that (so it would bottom-out at +4-7.5%). So a big fleet commander would actually want the fleet commander skills, and a big merchant fleet would care about the added cargo skill, and also a small fleet can get bigger bonuses.
(I also think that combat skills should give bigger bonuses to pilots in smaller ships. NOT huge bonuses, because that would make them really aggravating to fight, but like, an additional +5% top speed on helmsmanship when piloting a destroyer or frigate, something like that.)