Its typical for most RPGs that give you a choice on how to resolve an issue will, in general, present the more "moral" choice as being more beneficiary for everyone (player included), while the "selfish" choice will result in misery for others. Essentially karma exists, "do good and good things happen," but what of the "path to hell laid with good intentions?"
One of my favorite quest lines from an RPG is the Tenpenny tower, where an elitist community of, mostly though not all, racists hold up in a luxury hotel and refuse to let Ghouls (mutated humans) into their community. After persuading/threatening the most bigoted members of the tower to leave, and convincing the rest that Ghouls really aren't all monsters, the tower lets the Ghouls in. A few days latter the Ghouls kill every single human in the tower at the behest of their leader.
You did the moral thing and the world is a worse place for it.
Now I know if every quest line was like this, a game would get awfully depressing really fast, but isn't one or two in a game at least break the monotony of everything going as the player wished? What about the rest of you, is having a few quest lines where cause and effect trump good intentions something you'd like in this game?
Fallout is classic. One of the reasons why KotOR II is one of my favorite RPGs of all time is entirely because of the dark overtones and the moral ambiguity.
The best example I can explain was the first time the Exile travels to Nar Shaddaa aboard the Ebon Hawk. Kreia is mentoring you and you come across a beggar early on. He asks for credits, and being a compassionate and understanding Jedi, you give him some and he thanks you. Well, beyond your control, he is then intercepted, mugged, and beaten by fellow beggars who saw your generosity and took advantage of him. You attempted to do something positive, and yet something negative occurred as a result. Kreia has many talks with the Exile over the period of the game how blind kindness and compassion will not lead to a better galaxy or salvation. The Force, according to her, was far too mysterious and worked in ways no one could truly understand, making the world truly frightening and unpredictable.
There was also another great example in KotOR I when the main protagonist
comes across old Rakatan technology protecting a Star Map on Kashyyyk. In order to access it, you must answer a variety of questions presented by the Rakatan computer to you. He poses a variety of moral dilemmas during the life of Revan, a famous Jedi Knight during the Mandalorian Wars. One of the most memorable questions is there was a large Mandalorian force heading towards a highly-populated city. Revan had only two options he could make. He could attempt to defend the city from Mandalorian attack, but this would leave the Republic in an unfavorable situation and the war would go on, giving the Mandalorians more opportunities to kill millions, if not billions. His other option was to let the city fall and the Mandalorians massacre millions of innocents, giving Revan the opportunity to flank their forces and severely cripple their offensive, bringing the war one step closer to an end.
So what's the better option? Trying to save as many as you can at the time, knowing more battles will likely happen and kill just as many anyway? Or allowing innocents to die without help for the hopes of gaining a tactical advantage to end the war more quickly? These are true moral dilemmas and there really are no right or wrong answers, as many will die either way. Revan chose the latter, and because of that he was fortunate to cripple the Mandalorian offensive and ultimately bring the war to a close, killing Mandalore the Ultimate.
These are the kinds of choices I appreciate. Being good in a world were there is no good. Making tough choices that nobody should have to make and having to live with those consequences. What truly defines a hero is his greatest villain. Great leaders can only be found in times of great crises and when a nation is at its most bleakest moments. This is what defines greatness. It's time BioWare start providing more moral dilemmas so we can truly be heroes in our actions, and not just by our titles and NPCs praising us.