That's a good idea. Reputation is about the only potentially negative attribute in the game. I think they're avoided because it takes control away from the player.
In Deus Ex 2: Invisible War, you can get bio-augmentations (like skills). You can get them form official sources, or on the black-market. Those on the black-market are stronger, but come with side-effects. They (Ion Storm) are hoping that this will let the player play a light or a dark character.
