Legendary Apocalypse
There were no mods for this on the nexus so I spent a few hours modifying leveled lists in FO4Edit. On top of replacing every enemy with its corresponding legendary variant, it also replaces weaker enemies with the closest legendary in level. This means that regular Bloatflies will become Legendary Black Bloatflies, etc. So at a low level you may see some skulls.
There are two other things you should note. Firstly, melee super mutants and melee raiders do not have legendary versions. So they are replaced with legendary gun variants, who may still use a melee weapon if they spawn with a legendary one. Secondly, some versions of enemies such as minigun super mutants and missile launcher super mutants also do not have a legendary variant, but are not replaced. So they will be regular enemies, with miniguns and missile launchers.
Also, for now this only affects leveled enemies. So certain enemies, such as the bloatflies in Sanctuary, will not be legendary.