Please keep your suggestions concise, without expalanations so people can just easily browse over them. One-liners at most.
For me:
1. Chain of command for the General of the Minutemen with ability to order them on random quests
2. Drummer Boy-like person for the Minutemen
3. Ability to build underground in settlements
4. Territory control to keep cleared areas clear for good with manageable patrol squads
5. Vertibirds for Minutemen
6. Boats for supply lines and vertibird-like travel
7. Ability to mark objects as owned by the player so settlers will NOT use them
8. Ability to unassign-all for a settler
9. Ability to mark objects as "only I can assign" so settlers don't automatically use them
10. Ability to create templates for settler's inventory
11. Ability to remove corpses and bury settlers and your spouse
12. Ability to modify all of an item if you have multiple ones in your inventory
13. Ability to enter an amount when managing how much of an item
14. Ability to lower your weapon in first person view by pressing a button
15. Ability to scrap legendary items
16. Ability to take prisoners and ransom them for caps or use them for labor/research?
17. Set doors/gates to close automatically after a few seconds so settlers stop leaving them open
18. Can use an APC to act as a fast travel vehicle that spawns Minutemen/Brotherhood at location with you
19. Separate section in inventory for keys so they stop clogging up Misc section
20. Less naked NPCs