I for one don't. It seems like the moral dilemmas stop happening once you 'decide' your alignment.
I liked it better the way it was in Galciv 1, where your choices directly affected your alignment. Choosing it seems so gamey.
In fact, all you have to do is save 10 000 bc, take all those nifty +46% planet quality and +35% research bonuses that pop up, and choose to be good regardless. Or neutral, because it has more pros to it imo.
That, and the evil weapons are grossly overpowered. It's no fun to play the game when one of your frigates has more firepower then the entire enemy fleet. They should cost substantially more.