I hate Humanity Loss. I dislike it as a player, obviously some would say, but also equally much as a GM.
I consider it a tacked-on, artificial, heavy-handed, and boring, mechanic, which serves no purpose beside being a balancing mechanism.
I recognize my experience with the cyberpunk "source material" is fairly limited, but personally I can recall only one non-RPG cyberpunk setting, among the two-dozen-odd I"ve seen, that such a concept actually appeared in. So I disagree that Humanity Loss as a theme is somehow essential to cyberpunk stories, or that it's somehow a traditional, required element for cyberpunk settings, both of which I've seen sometimes tauted as a justification for it's inclusion in some form in basically every cyberpunk RPG game I've seen.
I can intellectually understand the need of some game masters for a balancing mechanism for cyberware, even if I don't fully agree - certainly, I have never personally felt much of such a need in my games. Humanity Loss, however, goes about providing that balancing mechanism in the, for me, worst, most sensibility-offending way possible - by interfering with a character's, PC's or NPC's, personality. This is something that should never, ever, be done. The player should be able to play a character as human or inhuman, social or anti-social, emphatic or cold, as they want (and the GM allows), regardless of how much metal they did or didn't implant in their body.
Certainly, a character who truly is, or even only feels, alienated and dehumanized because of their cyberware could be an interesting theme to explore. But it should be done how and when the player wants it, not as dictated by some dice rolls.
Even more so, because the default rules for HL have it always result in the same, identical, behaviour - homicidal hate of humanity. The human mind is an incredibly complicated system. It can break in a million different ways, dependant on a million combinations of triggers and circumstances. And yet everyone over-implanted with cyberware, regardless of their base personality, age, life experiences, social circumstances, type of cyverware installed, etc. goes crazy in exactly the same, identical, predictable way? I call bullshit, plain and simple. It completely breaks my suspension of disbelief (and yes, I am yet still able to suspend my disbelief of people cutting off perfectly healthy limbs to replace with machines, so sue me).
Of course, if you like HL, it's perfectly fine for you to have it in your game, this should really go without saying. But show the same courtesy to me, and don't try to tell me that I'm "doing cyberpunk wrong" when I remove it from mine.
So, now that I've ranted at length about how and why I dislike Humanity Loss, what would I do instead?
I usually enforce some kind of maintenance rules for cyberware. Not particularly harsh ones, but enough to make their presence known. You may want to skimp on routine meaintenance for your car, for example, but when it's your heart, you tend not to be as cavalier about it. I don't even really consider this a "control" or "balancing mechanism" for cyberware - it's just basic world logic and versimilitude. Machines need maintenance, or they wear down and eventually break down.
Similiarly, the world itself reacts to characters with cyberware in the appropriate, logical ways. High security locales have ways of detecting implants, the police will become interested if you display potentailly dangerous 'ware in public, some people may react negatively to you simply because of your implants, just like some do today because of piercings, things like that. Again, I don't consider this "balancing" anymore than the real world has a "balancing mechanic" for guns, for example.
If I felt like going beyond the above and introducing some true balancing mechanic (that would still be setting and theme appropriate), I'd go with something like what they had (in story, though not in gameplay) in "Deus Ex: Human Revolution": cyberware (beyond maybe the simplest things, like dental implants) requires the user to regularly take special (expensive, may be in limited supply) medicine, or else it begins to get rejected by the body, especially the nervous sytem. Which, of course, would cause the user rather big health problems. Something like that.
That's my stance on the subject, anyway.