I completely agree with the point that much (but not all) of cyberpunk has been about the dehumanizing effect of technology and the changes technology brings to society and culture.
What I object to is the game mechanics intruding in unbalanced ways. If technology is dehuamanizing, why is the only time it has a (game) effect is when someone inserts parts into your body? Or why is the body modification the only dehuamanizing technology?
I don't like the system in D20 because it is one of the few places where characters must take flaws or limitations for new abilites. This works OK in point buy systems (e.g. GURPS or Hero) because it's part of the game mechanics. But in most cyberpunk games it is an additional set of rules. And it goes back to the debates on adding flaws, drawbacks or limitation to D20 system, that they are simply munchkin bait.
Finally, I don't like the roleplaying restrictions imposed by the sytem. No, I don't like alignment's either.
Not to be completely negative, here is a suggestion for a substitute system. Instead of using Charisma, use Consitution for the Self score. As you add cyber implants, the meat gets replaced with metal or nano. When you run out of self, all the meat has been replaced, leaving you a complete cyborg. Now we need rules for cybogs and robots.