The real problem is that they gave no benefit for being neutral (grey), so you could play each piece of the story according to the situation. It forces people to go to extremes just so they can max the light/dark points for the perks.
It's much less fun to play a story when you feel like you have to be completely good or completely evil at every given moment. The choice, it seems, is just the facade, masking what is only our end game fashion.
Disclaimer: This post is meant to be taken lightly.