I think it would be super neat if the different sub-factions had rules that matched up with their in game counterparts. I've only played Warhammer 40k table top so I'll use the rules there as an example:
The mephrit dynasty for the necrons gets an extra armor piercing value added to their weapons in the tabletop game. maybe the meprhrit subclass gets a small bonus to weapon damage against armor in Battlefleet 2 to reflect the devastating nature of their weapons.
The Salamanders are large fans of flamers and melta weapons which are excellent at close range. Maybe their boarding actions are slightly stronger than other space marines chapters. (This may be better suited for Blood Angles but you get the idea).
I don't think these changes should be nearly as significant as the main faction you choose and what ships you bring etc, but I do think small changes like this to sub-factions would add a lot of flavor to the game.