Expanding on my previous thoughts regarding giving settlers names, I think you should also be able to set their personality, hostility and/or targeting priorities, plus give them patrol routes and advanced AI (yeah advanced AI in a Fallout game.)
Also i've only just become bugged by something that hasn't bothered me since the game released - the fact that settlements have a boundary and anything outside of that cannot be scrapped for parts; "oh look there's several trees just outside of the base but just because there's some insivible, predefined green boundary here I can't use the wood from them. Guess we'll just have to go without those fences."
I had the idea that settlement borders were a bit more flexible, perhaps rather than having predefined settlements you can just choose a location somewhere in the world, plop down a marker that creates a sphere of influence which you could adjust to suit your build, expand it out to be quite large and claim more territory. Either that or have the option to scrap things outside of your settlement area.