So the idea is to import the Humanity/Morality system from WoD into SR. You can even do this whole cloth, considering that the only difference (superfically) is the die type, and thus TN.
My idea for doing this is rather simple. We just finished a stretch of a WoD game, and I love the fact that in the "new" WoD all things have a moral compass or core, if you will. While I'm sure some people see these as limits on their gameplay and RP, I view it quite oppositely.
But why include it in Shadowrun? It changes the game, dramatically. All uses of that word apply. Instead of simply shooting peopl in the face for nuyen, there might be a bit of (gasp) thought. It makes it not just one big blob of grey, but the muted tones of light greys versus the dark greys. White areas would be virtually nonexistent, and the occasional black spot would be utterly evil.
While my familiarity with 1st ed. is none, I'm sure the woes of cyberware were lamented there as well. The detachment. The inhuman nature that comes with too much. The eventual degradation of the "soul" that comes with the concepts of no longer adding machine to the man, but man to the machines. My idea for this isn't a potential loss, but a simple reduction in your cap (typically 10). So your average shmoe on the street won't be too bad off. At the worst, they are just like every other jaded S.O.B. out there, apathetic and indifferent to the plights of their fellow metahuman. But for your hardcore Street Sammie, skating that edge, and boasting an Essence only remaining in decimals, they definitely would act different. They would lack the fundamental connections, and the ability to make them, largely, to the rest of society at large. This would be an actual mechanic (aside from a couple of Negative Qualities mentioned in Augmentation) that really bring this home.
For your more... out there magic traditions, this could also be a guide. Dabbling in toxic/insect shamanism could be a simple as one day you wake up crazy and want to destroy the world as it is known, but it might be a process. As you slip (lose Humanity) your behavior would change. It might be a means of throwing clues to PC, or again a game mechanic that makes their madness all the more concrete.
It's an idea, anyway. Thoughts? Concerns? Awesome nacho recipes?