Note that some information I supply here is definitely non-canon to LoZ, but the point of the idea is to incorporate these ideas with the zelda canon to make it fit.
Topics about a new LoZ game surface all the time on /v/, and one of the better recurring ideas is to make a game in which the 3 goddesses create the original hero of time, and give him a choice of the triforce piece he wants. He comes from a small village where he is different from everyone else. Kin to the way link can grow while others cannot, the hero of time is male while everyone else is female. He recognizes that the strongest piece is the triforce of power, and decides that this piece would be his greatest chance to rid Hyrule of evil.
He then sets out on his quest to do just that, rid hyrule of evil. He kills octocrocks and likelikes and what not, and goes through 3 temples before he stumbles upon the sword of time, which he attempts to pick up and fails. He is angered because he was told by the goddesses that as the hero of time, he would be able to wield the sword of time, but the goddesses explain that he is not yet ready to wield the sword because he needs to go through a series of trials to purify himself. Although this angers him, he continues on his quest and goes through those 7 trials.
On the way, it becomes clear that the protagonist's morals are severely skewed. He beings to punish and even harm citizens who are greedy, are envious, are prideful, etc. He gets Light-syndrome (if you read death note lol) and his definition of "evil" starts to incorporate far more than just evil beings, but those who he does not feel deserve to live with their sinful ways.
He decides that he will create a new Hyrule in which these evil doers are punished. Through the last four or so temples he goes to, after defeating the boss of the temple, he enlists their aid in his new world. After finally finishing the seven temples, he goes to pick up the sword of time when it has been moved. The goddesses tell him that he has become evil and out of their control, and he cannot have the sword. He then opts for a larger, more powerful sword of his own making and tells the goddesses that he wants the other two pieces of the tri-force, only to find out that they have been distributed to two unknown people. In his rage, he embraces his new destiny to find the other two pieces of the tri-force. When embracing this rage, he is able to achieve a higher form, one of pure power, of a boar creature. He assumes that this is his true power, and a sign that he is truly on the right path.
He then goes around Hyrule as the representative of his desert village and sets various obstacles for the other two unknown wielders of the triforce, such as poisoning the Great Deku Tree, enlisting in the help of his previous enemies as his new soldiers (known to Link as evil minions), and tricking the foolish and undeserving King of Hyrule out of his position.
He is last seen in his chambers as the ambassador to his village at the castle, playing an eerie piece on the organ, contemplating whether he is truly good or evil. He realizes that he is being watched by a fairy, which immediately scatters away towards the Great Deku Tree. The tree tells this fairy to awaken the new Hero of Time, who is to stop the old one who lost his way.
Of course, the game ends at the beginning of LoZ: OoT, and the player fully realizes that he has been controlling the "evil" Ganondorf. The game could be fun in that while Ganon is slowly becoming more evil, his clothing slowly changes from the green garb to his black and dark chains and cape, etc.
it would be great fun.