Whether by deleting them or by scrapping them, is there a way to remove them?

you can scrap the absolutely unusable ones but most cant be changed, that's kinda annoying since they make for some pretty poor looking ruins

Yep, just the ruined ones. there really isn't a clear flat area to build except for maybe the Drive-In. even that isn't totally flat.

The castle is pretty flat if you have made it that far into the game. If you scrap the totally ruined houses in Sanctuary you can rebuild on the old foundation. It isn't a perfect fit and that does bother me but nothing can be done about it..yet. I am hoping with DLC or a mod that we will be able to flatten land before we build and also I would love to be able to get rid of the bushes that can't be scrapped that clip through the floor that really bugs me.

I haven't tried yet, but you could potentially remove the houses using the console. I think 'disable' should do the trick. I used that remove annoying scenery objects and furniture in Skyrim houses. I did try it on the bushes, but I couldn't get any of them to target properly, even the hedges with collision... so it could be a lost cause. If someone can dig up the PRIDs, that could work, but I don't know how to find that without mod tools. I really do wish we could scrap them the same as ruined houses.

Agreed, I love those precious ruined house foundations! I'd love to have some large foundations in the prefab section. Hopefully once we get modding tools, adding various existing objects to build lists will be relatively easy. Those big house foundations could be quite useful! I'm surprised we didn't get more pieces to play with... lack of foundations and double high walls is an oversight. The raised floor sections make nice foundations (one even has a proper cement foundation, making it super useful as a wall even). They drive up the object count pretty quick though...which I've bypassed, but I still try to conserve object count whenever I can.

Even just the means to repair them would be nice, and remove/move the perma corpses.

I must be the only one that appreciates a good rugged and uneven area to build on. Shanty towns only look shanty because they're built haphazardly all over everything without much of a plan. For Sanctuary (after about a half dozen character restarts) I connected a wall between the the garage/workshop house, around the next door ruins/flat until the next standing house. Then from the opposite corner of that house, past the jungle gym to the hedges. Within this fort I built my shanty town, and a bit of a shanty palace on top of the garage of the workshop house (mostly, a barracks for even moar beds.) Now I just need to start modifying shacks to be multiple stories, and to get stairs up to these shacks without consuming too much space. Is there a settler limit? Trying to cram a bunch of subjects settlers into as controlled safe a place as possible.

10+charisma per settlement. Charisma boosts count IF you can keep them up long enough to bring in the new settlers (outfits shoudl work fine). Also, you can set your charisma arbitrarily using the console commands (if PC version) and get as many as you can handle on the system....caution advised.

I do like the rugged settings to start with. I'd like to be able to advance over time though and at least have walls and roofs without holes in them. Even shanty towns tend to have patched holes. I want to go from ruins to Kowloon 'walled city' eventually!

You can also rebuild the mostly destroyed ones, just add some walls and furnishings.

Excuse me but why has a mod moved this simple question to the spoilers section? I do not want to read spoilers, thank you! I was just looking for a yes or no answer.

Now I have to ignore this and search elsewhere.