The mods are not made the way you want because the modders don't have the GECK yet! We are limited in what and how we can do stuff. We can't create quests, New Lands, New Interiors yet. There is limited possibilities for scripted mods which are all required for the deeper mods your looking for.
I've been here all night Advocating for Console players to get everything that PC Players get! Talking to people sharing what information I have. (as little as that may be) statements like this and well some above make me kind of want to jump ship!
Edit: Your statement implies a sense of "Entitlement" which is a big part of why PC modders don't want to deal with the console crowd!
" want to be able to repair things over time and clean up overtime. I want a natural change over time. not a sudden change."
This also goes into showing that you have no clue on what it takes to make a mod and have never tried to make one yourself. Things like this are much more complicated then just copy paste. it takes scripting, conditions and possibly even the use of globals to alter the game world over time.