In Final Fantasy 7, I really wanted to help Sephiroth. He sounded like he had a good plan on making the world, ultimately, a better place, and its not like anyone is really dieing because they get reborn through the life stream in sort of a reincarnation sorta way. So I think an interesting alterna-plot is Cloud and party, tries to run interference for Sephiroth while committing various acts of eco-terrorism, sabotaging/fighting Shinra, etc. The game ends when the world is wiped clean and is reborn in glory.
Also, Fallout 3, it would have been nice to side with the Enclave rather than do their bidding for like one scene, and then with Broken Steel you could either be aligned with the brotherhood or the enclave based on your actions in the main game. Again, I think they had the best chance for bringing order and prosperity to DC, granted they had some pretty unsavory methods, and no reincarnation rationalization there, but I'd put money on an end to the raider gangs.