Currently, only some Chaos and Ork sub-factions have unique skills and abilities. I think its safe to say most people want more of this. Farsight Enclaves and Ynnari are the most prominent ones in my opinion. Aside from those, i think all races should have atleast 3-4 sub-factions with unique skills.
White Scars: They like going fast. Very fast. They could have a skill which increases their speed or gives them more energy. As an, ability maybe something that increases the speed of ALL ships for a small time.
Farsight Enclaves They are somewhat braver and a bit more eager for close combat. They could some abilities that increases their boarding capabilities.
Ynnari I am very suprised that this sub-faction didnt had one. Resistance to moral damage or troop or ship regen maybe?
These are just 3 examples i came up with. Please, give us more sub-faction skills