The idea I had for my setting was to base the cybernetics rules off of the FX item limits as far as what can go where, and a level system of the cyberware for how much. Cyberware would give interaction penalties, as the level of cyber tech really wouldn't allow for much to go hidden. My setting also includes Psionics, and any cyberware prohibits the use of any psionics in the character.
To balance all the effects of cyberware, I'm expanding Psionics with more powers, and advanced classes. The only problem is for players who don't want either cyberware or psionics for thier characters.