Why is amnesia always brought up as a bad thing?
The point is not if the plot includes amnesia or not .It's how the amnesia plot device is used. A good example of this would be the film Memento.
In the specific case of Torment, amnesia allows you to have a deep and interesting lead character that, at the same time, you can role-play as you see fit.
And this is something I had never seen in a rpg before.