This is a pity, actually. A bit more variation in the MM radiant quests, a bit less hassle - the MM idea is actually quite good I think. I hope, they fix the various problems with quests and building.
Also a DLC or a bigger update for MM would be fine. I would wish for:
1) More MM NPCs (the guys you call with the flare gun). You - as the general - should be able to help with their equipment. If you have Armor/Weapon stores in your settlements it should make the equipment of MM and maybe settlers better.
2) General 'morale' could be affected by number, size and happiness of your settlements. More morale means higher levels of the MM NPCs.
3) Trading in settlements generates more MM, you can call them more often. It should be limited how often you can call on them.
4) New additions to settlements become available if you have more settlements and more average morale (happiness).
Also I think the animations - while they play no real role - of the settler NPCs should be worked on. Somehow the nameless NPCs in Goodneighbour or DC look better, more natural. Settlers stand around too often. They go to the bar in the evening, and to their beds, if they can reach them. (I have 16 in Starlight Drivein, and no beds assigned, but they all walk to the house and use the beds, this seems to work). But they look peculiar in the bar - they too often stand up and change the seat, this looks awful. Also they should 'use' the items in the settlement (work benches, etc.) like the named NPCs do. And they should visit the settler shops, it looks awful when the settler merchants stand the entire day and nobody except the player visits.
I think the settlement system should have more rewards, when you do it better. Nothing big and unbalancing, only small things. Then we players would be more motivated to build up our settlements, and not concrete fortresses but just how they were planned by the devs.
Edit: When I write 'using the shops and work benches' I am talking about unassigned settlers. There will always be 2-3 at least. You can have 5 settlers assigned to shops and you need around 4-5 settlers for food. If you have 5 guards, and one scrapper, then with a maximum of 20 settlers (more makes no sense) you will have several unassigned settlers. They could make the settlement more lively looking.