Ok, recently I got to messing around with fallout shelter. I find the game fairly addictive. And got to thinking what bits about it I like the most.
Sending out wanderers to get supplies. - Modding that should be simple. You could either:
1) Send the person out in the wasteland, and roll some dice in the background every now and then on what they find, or what attacks them
2) Send the person into a cell outside the game (where nobody can attack them), roll some dice much like option one. The added benefit is you have more control on what happens to your npc
Personally I am of the opinion of option one. Have a script that picks a random path for your npc, as he/she follows it random encounters in the world will happen. Have another script where your explorer loots up any dead bodies, and continues on his merry way. It would give you great incentive to load your explorer up with lots of stims, rad-away and guns.
Building downwards:
Settlements are nice, but a vault would be neater. In theory it should be possible. You would need to create a unique set of materials, for the walls, and the vault door would zone you into your new cell.
Jobs:
From what I understand, the settlements already has some of these features, but it will likely need to be expanded. Like a job of a higher level npc to train lower level ones. Or rooms that increase npcs special stats. Or a nuclear reactor where if you mistreat it, it might convert some workers into ghouls.