Visual fluff, like for example, synth could craft special legacy armor where you can choose the color of the armor, same for armoring, etc ...
Some legacy only skill:
there could be several type of legacy skill tree, and you could be able to choose only one of them. I don't want that those skill tree to be dps/heal related, but more for buff for example.
Be able to use the companion of any member of the legacy . ("You're in love with Mako ? no problem, a couple of mind trick and she will be in love with me Nyahahaha!")
Indeed shared cargo hold, a must have.
Being able to use the ship of another member of the legacy. ("I am the boss of that legacy, you give me your ship or i make you suffer with my lightning Nyahahaha !")
Being able to have all sort of relation between character and having title related to them (everything from slave to grandmother, including concubine )