I'm not sure if this has been suggested, sorry if it has.:)
Anyways, My idea was to customize ships in either increasing their Speed, Power House, Turn Rate's Etc Etc with buy-able upgrades.
But to stop people just stocking up on crazy amounts of upgrades, Limit the amount that they can buy by only have a limited amount of space to put them, like hard points.
EG: Say a light fighter can only carry 4 upgrades you could arrange them either: