I want to expand on this request a bit.
We have the 4 main factions (BoS, RR, MM, and Inst) but the MM are the only faction to actually "control" settlements and allow you to build them. Now, if you can align each settlement individually to a faction, then you can set p supply lines between settlements that are under control of the same faction.
For example, you've unlocked Sanctuary, Red Rocket, Abernathy Farm and Gray Garden. You've played far enough to be a "member" of all factions, but not far enough that any kick you out. You align one settlement to each faction (MM>Sanc, BoS>Red Rocket, RR>Gray Garden, and Inst >AF), but you can't assign supply lines due to this. Next, you piss off RR, so you take Gray Garden and align it to BoS, and now you can establish a supply line between Red Rocket and Gray Garden, but not the other 2. And depending on what faction the settlement is aligned to would unlock something in the special menu.
Bos would give a Vertibird, MM would give Artillery as normal, RR would give a "Supply Drop" that would randomly restock with food, water, ammo, weapons etc. The Inst could give you a the ability to build Gen 1 or 2 synths like to how you can build robots with Automatron installed. If you are considered an enemy of a faction and there are settlements that are aligned to them, that settlement becomes hostile to you and you can regain control of it by killing everyone and retaking it that way. Or they could stay friendly with you, but you have to convince them to join another faction before you can continue to build the settlement up.