A bunch of skills do seem like a kind of nice idea. At least I enjoy the feeling of *improving* over time and having more difference between players with skills supporting their individual playstyles. Still I do think that the effect from skills should be mostly kept quite small, but still slightly noticeable. At least the skills concerning ship handling.
Bartering seems like a nice idea, skills involving black market/counterfeit goods could be nice too ( lower prices there, a slightly better ability to hide them from police/equivalent ).
Some other ideas:
hacking: making the ship ai more robust, improving the targetting of the turrets and other automated stuff by few percents
engineering: being able to rig the ship to fit yourself, squeezing some extra power from the ship in exchange for reliability, skill affecting the ratio
leadership: how many ships you can have under your control