If this is the apocalypse and people are pushed to the brink of sanity, then why is everyone so clearly "good" or "bad?"
There are hints of actions, characters, and stories within the game that the outcomes are unclear or your actions are morally grey i.e. the quest with "mysterious meat snacks." Is that enclave 'actually' cannibals and murderers or just great at masking unknown meat? It's never fully revealed. Also, Red Talon, they are the epitome of an edgy, morally ambiguous faction yet actual gameplay only shows them being the "good guys" when we all know they aren't necessarily your friends, especially if you were to suddenly stop furthering their end goal.
I think it could add tremendous amounts of replayability and depth if morality was heavily expanded upon. Your faction can have a karma slider, allow us to be the bad guys and betray other enclaves or exploit them for resources. Other factions have more depth and motives, as well as interact with one another more (if you help one faction another one may dislike you, one enclave may fight another, etc). Individual characters also have more depth and motives, maybe even betraying your faction, trying to usurp power from your leader, or just leaving if they disagree with your actions (think about how devastating it could be to find out your new favorite community member had plans to steal resources and betray you since they joined you). Add morally ambiguous questlines where we never find out whether we made the "right" choice or take away many of the "right" choices all together as it's more realistic to have no good choice in an apocalypse. Quests can also be expanded upon by adding real consequences to our actions which only appear later, if at all (that unique sniper rifle we snagged in a Valley supply cache actually belonged to someone and we only find out after/if we move to the Foothills and they are angry we took it because it was their sister's and now she's dead because we took it).
These are just a few ideas to expand on morality and hopefully create a more realistic and emotionally impactful experience.