[/QUOTE]My advice as to what NOT to repair would be to avoid raider areas like Corvega, Saugus Ironworks and Lynn Woods, and Super Mutant areas like Breakheart Banks, Fallon Department Store and the Coast Guard, because these groups are not fussed on their areas looking NEAT UND TIDY, and it will help identify their areas once your mod is done.
I'd also leave Fort Hagen, because that's one guy holding the place, and it'd be safer to just leave it for the main story.
I think, though, that cleaning up Gunner areas would be good, like Quincy and Gunner's Plaza, because although they be heartless mercs, they are still people with a chain of command that run in a military way. Even the military has people who dig the latrines and build the defenses.
And, going off on the story subject, Raybo is correct that not all of us are technically minded, but instead have a gift for imagination. But, like your proposed mod, stories need planning as well. Like mine, https://simsettlements.com/site/index.php?threads/manifest-destiny-creative-story.11643/
Even though I'm only three chapters in, I have it planned up to 30, because I hate being backed into a creative corner :P
It looks like, however, you've got a head on your shoulder and have given this whole thing a lot of though, and I'm certainly interested to see what you do :D
Assuming I have the skill, a big IF the areas you mention will be......mostly untouched. Hostile faction WILL control Lexington AND will heavily populate the Corvega factory, To my thinking, the Corvega factory will no longer make cars as such: bit it will be salvager workshop, with disassemblers, plasma smelters robot production with material moved from General Atomics Factory
In a post-apocalyptic world with general-purpose worker bots, the wealth of a community depends on its ability to turn scarp into worker bots, because worker bots are tireless if unimaginative slaves that can make things from pre-loaded templates to very high tolerances. Workers bots, given the right resources, are self assembling animated capital. Assuming the Corvega plant has it's own power source, and it almost certainly does, you can manufacture almost anything with the right machines as a stopgap. So Coverga Plant, the interior is going to be completely different in the interior, and the enemies will be different, but as a raider/Gunner stronghold it will still be a blast to shoot though.
Also, it has the prize of a machine that dissembles what is put in it, armor, weapons, junk. Weapon mods return their full material cost and things that can't be built you get DOUBLE of what you would get out of Scrapper 3 (based on the notion a baseball statue costs 10 copper and with Scrapper 3 only 5 can be recovered) as well as a robot crafting station