Think EQs/WOWs weapons skills, Kinda like that maybe? But each captain has their own set thats starts off anywhere between say 25% to 65% (but all the stats start off at different levels say one has navigation at 37% and gunnery at 54% when you first get them) and as you use those skills they level up say if you manually destroy a very very fast ship with a slow weapon, would give bonus to that skills level progression than destroying the same ship with a fast firing weapon, for those rare times you can actually do it.
or even have different weapon types use different skill types and have those all total into your overall gunnery skill? Which means you can spec into say engery weapons and not missiles or ballistic and still do well even with a lower overall gunnery skill? And say at certain points in that skills progression (if you placed a cap on it per level, like 100 for lvl 1, 125 for lvl2 so you dont get to like skill 400 at level 4 or something, to keep it balanced) you unlock a certain amount of perks which each level gives you a number of perk points (more per level past a certain point since gaining very high levels would take longer, there should be a better reward for getting to them then say lvls 1-10) and you could pick a perk from that tree (maybe only one or two perks per skill level tree so you cant just get all of them at maximum level, you have to do trade offs)/
It would foster more of an attachment to the players own captain along with the ones you hire, keep alive and level.
(Quickly throw together sample, if more people like it, ill try throwing together a MSPaint version of it with more detail {'s mean the total skill level required for said perk. Also maybe allow us to see perks within 50-60 points of our current skill level, so we might be able to plan which perks we want to get later?)
Gunnery 64/100 Perks [+10% to fire rate{25}, +5% laser/kinetic/fragmentation/HE damage(drop down list of damage types to pick from?){50}]
Navigation 46/100 [-15% FTL fuel consumption{35}]
Shield operation 52/100 [-5% damage to shields{25}, +10% shield deployment speed{50}]
Armour Fitting 45/100 [+5% Armor damage absorption {40}]
Salvage 37/100 [+5% better chance of saving a disabled ship from being scrapped {35}]
Engine Tuning 35/100 [+3% faster combat and/or travel speed{35} (maybe another drop down menu to pick from?)]
Hows that?