I have a few:
- Chosen ones, fate, destiny, &c. When you get down to it, a story with these themes is one where a single person or handful of people is ontologically, cosmically better and more important than everyone else. It's eerily similar to that right-wing meme about how "most people are just NPCs" (though I disliked the trope before that meme ever took off).
- Way too much importance being given to bloodlines by the narrative (note, this is different from them being given importance by characters or societies in the story).
- All of the good characters are handsome and beautiful, while all of the evil characters are ugly and disfigured (with the possible exception of a femme fatale or two).
- Races that are inherently, unchangeably evil down to the last individual regardless of upbringing, society, or material circumstances.
I think the problem is that Pondsmith and others inspired by him still use the word "humanity" for it
In Cyberpunk RED, only implants that take you above and beyond what a human can do begin to affect your "humanity" score. Replacing a limb or getting cybereyes to allow someone blind to see doesn't make anyone less human anymore in terms of game mechanics - you don't get hit with a "humanity" penalty for it. If you start loading up on cyberware that begin to push you into the realm of (often violent) superhuman - implanted weapons, a reflex booster that basically makes everyone move in slow motion - that's when the stat begins to be affected, and even then it's meant to represent an alienation from others rather than becoming ontologically less human
It's a sight better than Shadowrun where even an implant that lets you taste food better will materially make you impure and less able to tap into the purity of magic, but it is still problematic. I think there's definitely a story that can be told in cyberpunk about being able to pay to become literally superhuman, and how that would inevitably cause class divide to be a literal physiological divide - imagine a world where every rich kid is literally smarter and faster and stronger than anyone else can ever hope to be unless they also paid up. The problem is most cyberpunk writers are lib as fuck and can't even begin to think about class properly, so instead of a discussion about alienation and paying to become superhuman, we get this garbage about becoming subhuman for modifying The Divine Form
The nitty-gritty of Shadowrun's version is actually pretty good - it's not actually the soul that is harmed by augmentation, it's "the ability of the soul to recognise its material-plane anchor". Thus most purely restorative things like cloned limbs or corrective surgery, and such don't have an Essence cost (or it's minimal), as there's no sudden disjoint - the astral form was always that way, or organically changes at a rate it can follow.
Essence loss has no real effect on characters IIRC (some effects on getting magic to work on you, maybe a bit of social stuff but with the same "probably the social phenomena of being a walking killing machine, and forgetting to turn off your Wired Reflexes in public" rather than soul damage), until the point that your astral form no longer recognises your body and falls off. This isn't presented morally, it's just a metaphysical phenomenon that can be understood in-setting and therefore addressed.
Advanced tech and magic was slowly beginning to understand how to create augmentations that respected this - geneware, symbiotes, nanotech, to begin with - and had even begun to work on a way to restore that connection (via using the Metahuman Vampiric Virus, which is capable of Essence restoration somehow).
The only real EEEEVIL cyberpsychosis was from the Cyberzombies, a crude and classically corporate black project on "we wanna make supersoldiers but they die if we stuff too many guns in their skull" where they "solve" the problem by getting Blood Mages to staple their dissolving astral form back into their should-be-corpse and add Forced Memory Stimulators to try and constantly trick them into thinking they're alive in between killing sprees. It's pretty fucked.
But I stopped caring about keeping up with Shadowrun with 4E (because of the embezzlement from writers, and subsequent scab takeover of the setting), so who knows how they present it nowadays...
Shadowrun 5 is the one I know best and unfortunately a lot of that's changed
Specifically, Essence is now tied to your magic ability and maximum social limit. The maximum Magic stat you can have is tied directly to your Essence, and the calculation for it and the social limit round down to the nearest full number, not caring about the decimal
So even if you were to get say, cybereyes to offset a character's blindness or poor vision, which I believe is 0.50 essence cost, you go from your 6.00 maximum to 5.50, but every calculation takes it as going to 5.00. One point isn't a crippling loss for a build but starting from <5 and you'll start to have trouble doing anything magic or social