I once toyed with the idea of the main character being a grunt soldier in a war against an ancient evil. The ancient evil can only be defeated by the "Hero from the prophecy of hope...or something" The twist?. Another person becomes the "Hero" while you remain a grunt the entire game. The "Hero" also never joins your party. Your party does not battle the ancient evil.
Honestly though, if I was to create a game I would probably have it as a country in civil war due to the lack of ability of the country's leaders. Three different storylines would be told with the ability to switch between them similar to Wild Arms if the prologue kept going. The order of choices you make would have effects for the other characters.
The main characters from the three stories would be
A young father going off to war in what he believes is for the good of his family.
The wife of character A who has to rally the remaining people in her village to fend off bandits who see her home as easy prey.
A high ranking officer for the rebels. His choices effect the outcome of certain battles.