Originally Posted by
Danger Close:
“Unfortunately not. You can put new furniture and decorations in them to make them look nice but not fix the holes or add doors (This Old House is now playing in my head. Jesus, I'm old 
). And only the ones that are just rubble can be scrapped.
I'd expect one of the first mods available will be a revamp of the settlement feature.”
To be pedantic, that's not entirely correct.
I can't remember where I saw it but there are plenty of videos on Youtube explaining how you can (if you really want to) renovate all the original houses.
Basically, it's a case of using a "exploit" in the construction options.
You can build a "wooden floor with foundation" right next to an existing house and then add doors, walls and even a new roof and then, when you're happy with the result, you can scrap all the new bits of floor you've added and just leave the walls, doors, ceilings and roof.
As far as the game is concerned they'll just be "floating in mid air" but to all intents and purposes they'll look like part of a pre-existing building.
It's a huge faff and there's no easy way to do it but it IS possible to renovate the original houses if you're really determined to.
Of course, there's no real need to.
Speaking of which, my settlement at the red Rocket was just getting too busy so I ended up just building a "compound" on a cleared slab in Sanctuary Hills and it looks very neat and tidy.

Basically, it's a C-shape of joined metal prefabs with a wooden roof over the top and then a fence across the front to stop settlers wandering in.
While I'm at it, I found another "bug".
I did The Battle of Bunker Hill a few days ago and fought my way through it all but then I found myself carrying too much so I dumped a bunch of stuff in a cabinet in Bunker Hill and then, when I came to retrieve it, the residents of Bunker Hill seemed to think I was "stealing" so they all became hostile.
I ended up reloading a quicksave and this time I decided I'd just complete the Institute portion of the mission so I killed the Courser and left the BOS, Railroad and Institute to their firefight.
So, out of curiosity I decided to go back into the caverns undern Bunker Hill last night to see what loot was left lying around and I discovered that all the machine-gun turrets down there are now indestructible!
I guess the game intends that they should be destroyed during The Battle of Bunker Hill mission and so it makes them indestructible at any other time to ensure they're there for that mission but if you don't destroy them during the mission they end up being indestructible forever.
I still can't get Piper her story about Mayor McDonaugh either.

Apparently, once the main story is over you're supposed to go to Diamond City and find a guard who's been shot by Mayor McD' because he's gone nuts after the Institute has been destroyed and that prompts a resolution to it all but it just doesn't seem to be happening for me.
The guards are all still healthy and Mayor McD' is still just staring out of his office window making random comments.
I guess with a game this complicated there will inevitably be some small things that end up "broken".