I think if executed well, moral choices are a good idea, but most moral choice systems tend to fall into the trap of "Good vs Bad."
I probably use it as an example too much (especially considering I haven't even completed the game yet), but Shin Megami Tensei has a very good moral choice system. Instead of Good or Evil, there are two distinct theologies present: The Gaians (Chaos), who believe in absolute freedom and anarchy, and the Messians (Law), who believe in absolute law by word of God. There's also the path of being neutral. Depending on your personal viewpoint, both sides could be good or evil. The Gaians are a bunch of wild, lawless anarchists who worship power. They're also people who believe in freedom and achievement through strength. The Messians are a religious order that wants to bring order and peace to the people. They're also a group of zealots who will leave you to die if you don't accept their God.
Your alignment has practical benefits and downsides, too. If you follow Chaos, the Gaians will welcome you, but the Messians will try to kill you will be unable to use Law demons. If you follow Law, the Messians will treat you well, but the Gaians will hate you and Chaos demons will be restricted. If you go neutral, all demons can be used, but everyone will be out to get you. There's also no obvious "Chaos" or "Law" choice a lot of the time, and the lack of any sort of gauge or indicator (besides finding out you can't summon a certain demon) forces you to really think about your choices.
In the end, it comes down to your own personal values and view of the world. If more moral choice systems were like this, it would probably make for much better games.