Well, Hyrule certainly prospered under Zelda's leadership prior to Twilight Princess. The kingdom encapsulated more land than ever, the people seemed to be fairly affluent, the middle-class and small business was thriving through the land. Under her stewardship the people were provided with a comprehensive sewer system and a reliable postal service which improved living standards and public health. Unemployment was also very low, close to 0%, and no one seemed to be living in dire poverty.
However, it was during her reign that the Twilight invaded and took hold of Hyrule with little to no resistence. Her self sacrifice was commendable but do we really want a leader who would rather surrender to avoid war or one who would fight for her people?
Ganondorf would be that strong leader in times of crisis. He isn't afraid to show a little (or a lot) of force and he would certainly keep Hyrule's enemies in check. Under his leadership, Hyrule would be able to project a formidable image to other lands and the people would no doubt be safer in general.
Domestically, however, I'm not convinced. Under Ganondorf's leadership, the Gerudo have virtually vanished from existence altogether. He single-handedly brought his state to utter collapse and I fear it had a lot to do with his economic policy. He favoured a system of 'looking out for number one' which left too many of his people destitute and heavily favoured a ruling upper-class elite, consisting of around 1% of the overall population of the Gerudo State.
In the end, my vote goes to Princess Zelda. There is a lot she could do to improve her foreign policy but she is a wise leader when it comes to domestic issues and I just trust her more. There's something about that Ganondorf I'm just not comfortable with...
