So, this thread has been dead for a good long while, but...
Armored Core 4: For Answer is just...wow. There are two paths that are remarkably sad, and then the third path. In one, you have to end up condemning humanity to a slow, gradual decline due to having poisoned the planet, as well as allowing the megacorps that caused that situation in the first place to get away scot-free. The second really hits hard. In order to ensure the future of humanity, you have to shut down the flying cities they built, and, in the epilogue, it states that your actions killed untold many people, including infants, and that, in the end, humanity won't change at all. I mean, DAMN.