When I had the option to kill (a particular thing) or not, I actually debated - how will (the being who gave me the quest) react? Which choice is better here?
When I made my choice, I was shocked to find that he wasn't disappointed with what I did. It was basically, "Oh, that's ok, at least you (did something").
That was very disappointing. Made me feel like sitting there thinking about it was a waste of time because no matter which I chose I'd get a slap on the back.
So yeah, one big gripe is, like you say, many things turn out the same way whether you take the "good" or "evil" approach.