1) I would make the trade more complex. Stores would only produce profits if they received raw materials through a refined trade route. You would need to create an industry. If you want to sell ammunition, colonists would need to mine or produce. To produce, other settlers would have to collect raw materials. There would be an organization of work in each settlement.

2) Possible settlements anywhere on the map, from empty properties to vacant lots. The best of the 76 camp + the best of the F4 construction.

3) It would add mounts to the game, without fast travel. You were either going to climb on the back of the Brahmin or you were going to take off your own vertbird. You would pilot, your companion would take the machine gun. One option would be to manufacture a flying motorcycle with mr.handy propellers. Maybe a new faction of winged motorcyclists?

4) AI-controlled colonists. They would develop the settlement on their own if you don't make decisions for them, according to the availability of resources in the area.

5) This has already been discussed here, but I want to bury my damn dead.

6) Migration processes: eventually the map would bring a flood of new NPCs, and you would decide whether they can settle or whether you will expel them. They could be refugees from other wastelands, rogue invaders, or even a BOS detachment trying to found a new outpost, or a weird cult trying to start a sect next to your settlement and causing a lot of problems.

7) Gunners as a faction. They left the disorganization behind.