The basic idea behind the moral choice system is sound: That the player get two different endings, or just two different sections of storyline, based on their feelings and decisions. However, most games fuck it up by expecting you to be either good or evil. The idea should be that it's a very grey area that expects you to weigh the sides, and make a choice you always weren't sure about. Kind of like "Should abortion be outlawed" rather than "Should babies be legal snacks at restaurants?"
Deus Ex did it perfectly. The ending to the game presents you with a choice, with a total of 3 possible endings. None of them are inherently "good" or "bad". In fact, your choices are essentially: Take over the world, or plunge the world into the dark ages again (no technology works, everyone has to start from scratch)
Phoenix Wright: Justice for All also has a very good cliffhanger decision, but I won't give spoilers.
Deus Ex did it perfectly. The ending to the game presents you with a choice, with a total of 3 possible endings. None of them are inherently "good" or "bad". In fact, your choices are essentially: Take over the world, or plunge the world into the dark ages again (no technology works, everyone has to start from scratch)
Phoenix Wright: Justice for All also has a very good cliffhanger decision, but I won't give spoilers.