You know what, here's how I would have done the story with fungus, monsters, transexuals, and cultists
Make the cultists troons
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Seriously you have a real rogues gallery of what to base enemies off of. I want some unsettling creepy troon motherfuckers. Since society has collapsed nobody can afford things like advanced medical drugs or razors. You now have a bunch of fanatics obsessed with vanity similar to how Bioshock's enemies went from normal people to freaks of nature trying to improve themselves. So these troon motherfuckers still want to be women because since society has collapsed they can now remake it in the image of a woman. So lo and behold the zombie fungus is viewed by them to be a way to complete their transformation and take their withered men bodies and turn them into beautiful forest nymphs who are one with nature. But they fuck up and the few who became zombies lose their minds and other shit so the troon cult leader wants ellie so they can try to have all of the positives of becoming fungus people but without the negatives, basically trying to make a female super solider of the mushroom kingdom and becoming princess Toadstool queen of the new humanity because fungus reproduces asexually so gender will be erased. So they make ellie out to be some sort of messiah and proof that men must be erased and the Troon leader wants to control her as leverage for the cult.
So not only will you have creepy looking and memorable scary bad guys, it would tie into all the elements of the previous game but it will give it a new twist. You now have a bunch of selfish motherfuckers obsessed with vanity and who want Ellie to give them something real shallow in a world where far more serious needs must be met. it's about as good a starting point as any to give everyone involved a drive that will last towards the end. not only that but some good ass body horror and disfigurement.