Moral dilemmas are good, but if this game becomes a reiteration of spec-ops: the line (which I never finished...), where the game forces you to choose bad choices and then proceeds to beat you with a giant sign that says: What have you done, you monster you... I'll just have to skip this one.
Indeed. I loathed that in Spec-Ops. It's just not effective to force players into bad acts if they want to proceed, then tell them they shouldn't have done it. What's my other options, stop playing and waste my money? Screw that.
I wouldn't be averse to the game exploring concepts of colonialism, honestly, and better than the good vs evil Avatar way of things. Say that the colonists need a ressource on a specific planet, but the technologically inferior natives also need it and aren't willing to give it away. Do you convince them to share (so less for you), move away in the hopes of finding other sources (with the risks that entails), or take it by force for your own survival (which means losses for you and generally being a bit evil)? That kind of moral dilemna.
I just hope the native races don't just turn out to be giant assholes we can shoot in the face with impunity because they're evil.