Here's one I've been wanting to do ever since the game came out, but I am awful enough at modding that there's zero chance of it happening without the Creation Kit.
My 2 big pet peeves with Fallout 4 are the whole skeleton's and the safe contents.
Skeletons:
While you might find whole skeletons sealed away in vaults, or other containers, where animals could not reach them, you should NOT find whole skeletons outside. Animals will eat them, or weather will tear them apart. Now it's been 200 years, many of the skeletons you come across might actually be the remains of other survivors who died only a few years before. But there are a few cases where the skeletons are very clearly meant to be the remains of people killed during the war.
So I want to delete them, or replace them with a few loose bones.
Safes:
Ok this is the one that really ticks me off. Why are their pipe guns in safes and containers in Vaults or other places sealed away since the war? If I go into a chamber that's been sealed away for 200 years, why is there a scrap-made pipe rifle in there? Who is going around to high quality safes, deep within military outposts guarded by robots, and slipping pipe rifles into them without touching any of the other valuable items stored there?
It's just lazy design or a lack of forethought. Easily fixed by changing up loot lists for those containers to only contain prewar weapons.