1) The abilty to dye clothing. I like my vault jumpsuit, but it'd sure look better in black or navy blue.
2) the ability to build armor and weapons from scratch. Since we've already established that I can make a generator out of some toy cars and coffee cups this isn't that much of a stretch.
3) Maybe add a 5th rank to armorer, gun nut and science and, if you have the right combination, let you add your own legendary effects to armor and weapons. My model here is the enchantment skill in Skyrim (which, for better or worse, this game is clearly influenced by).