We've seen the Legend of Zelda over the years made by Nintendo on just about every system except from the Virtual Boy. The story has been similar with the idea of Link stopping Ganon from taking over Hyrule and obtaining the pieces of the triforce. A few exceptions of the rule would be for Zelda 2 with Shadow Link, Minish Cap, and the Four Swords games with Vatti, Majora's Mask with Majora, and of course in Phantom Hourglass having a completely different villain. Looking closely at the situation, you have to wonder what else is there to do?
After Twilight Princess came out, what else could be done to enhance the story and how in the world can you bring Ganondorf back into the picture? My thoughts are leave him look to be dead and not even appear just for a change of pace or come out and declare him an immortal. Think about it, how many times do you kill Ganon and he keeps coming back? It's the same deal in Castlevania with Dracula, at least early on before the Aria and Dawn of Sorrow games and skipping Lament of Innocence. In fact, it also draws as well with Sigma from Mega Man X constantly coming back until X8.
As far as what to do with a new Zelda game, perhaps maybe a new villain that would be much different. How about an actual Dark Link character? My idea of the look would be black tunic, red eyes, holding a dark blade powered with an evil triforce dubbed the Triforce of Darkness. The idea really is that it would be more of a mirror world.
The plot would be something like Link has gotten away from Hyrule on a trip and gets sucked into a bizarre world. Now the idea is somewhat like how Superman has a backwards counterpart in Bizarro and it's like he's in Bizzaro World. There is no mention of Hyrule at all though it looks similar. The townspeople think Link is out to terrorize them because of Dark Link's evil intentions. In fact, some have been calling for their hero to come down and battle the Dark Link but the twist is that the hero looks awfully like Ganondorf. After a battle and defeating him, he doesn't deliver the final blow and makes the townspeople wonder why he wouldn't do such a thing.
Ok, maybe not the most idealistic plot in the world but it could work if done right. What was seen was the general idea behind it. The game itself will consist of eight dungeons and then going into a dark castle looking very close to Hyrule castle. The major boss would be Dark Link himself and it would be a sword fight to the end. There will be shadow link clones in the palace itself before facing off with the major boss.
If you want to add a special mode just for a different end, you could have it play as the guy who looks like Ganondorf though his name doesn't necessarily have to be that but should look like him for this purpose only. It wouldn't even have Link in it at all and just be a special mode.
Well, that's about it as far as a new Zelda game. It could work and be interesting but only if it's Nintendo making it. We don't need another incident with games like you saw on the Phillips CD-I designed to upset Zelda fans. This would be possibly a different direction as far as a different villain going and would be good to experiment to see what reaction you would get.
