I've kind of toyed with an idea that while I don't think it would hold up well as a full-fledged sequel, it could be a sort of "stop-gap" game that they could release between Zelda games.
Basically, what about if you had a Zelda game where you don't play as Link, but one of the random NPCs in Hyrule. Imagine playing as a guard in Hyrule Castle. Instead of a big sprawling overworld, you have the entire castle as your game world, but since you're just a lowly guard, you don't have the authority or permission to enter certain parts. For instance, they probably wouldn't let a guard-in-training or something enter a room like Zelda's private living quarters, a war room, or the parts of the castle used for delicate political meetings.
Ganon attacks, shit goes down, and you have to try and keep things together. Instead of unlocking new dungeons and getting better weapons, people are dying and as things get more bleak, the higher-ups are getting more desperate. You're suddenly getting promotions because the people in charge are dead and need replacements, and you're one of the few people left to fill the position. You aren't getting better gear from dungeons, but maybe the higher-ranked soldiers get better gear, and you make trips to the armory to outfit yourself with what you need.
The catch is, you're not the hero. Yes, you have training and actual armor, so maybe you'd start the game with higher health or stamina than Link would usually. However, while the "Hero of XXXX" has the support of the Sages and the Goddesses alongside the power of the Triforce of Courage, you don't have any of that. You aren't getting Heart Containers or stamina upgrades, you're just as weak at the end as you are to begin with. Even worse, you (the player) knows that Link is going to be the one to save the day with the Master Sword, which you obviously don't have. You know you're going to die, the final boss is simply trying your damnedest to stall for time while what remains of the Royal Family escapes to safety.
Since this would do best as a "stop-gap" game, like I said, you could do some really awesome stuff plot-wise. For example, let's say that this game took place around the same time as Ocarina of Time. Your role in all of this would be ensuring that Impa is able to escape with Zelda. You spend a good part of the game not only trying to keep them safe, but keeping the Royal Treasure away from Ganon's forces. In the end, you die, but Zelda is able to escape with the Royal Treasure. The final scene of the game would be the scene where you finally find out what the treasure was: you see the scene from Ocarina of Time where Zelda and Impa ride out of the castle, and Zelda throws the Ocarina into the moat for Link to grab.