Skills that give more ship Protection:

Shield management +5% Shields
Hull upgrades +5% Armor
Mechanic +5% Structure

Skills that give more ship Resources:

Electronics+5% CPU
Engineering +5% Powergrid
Energy management +5% Capacitor

Upgrades:

Shield operation -5% shield recharge time
Energy systems operation -5% cap recharge time
Shield upgrades -5% powergrid needed for shield mods
Energygrid upgrades -5% CPU need for energygrid mods
Electronics upgrades -5% CPU need for sensor mods
Weapon upgrade -5% CPU need for all weapon kinds