I look forward to seeing some of these suggestions in action, considering Nintendo has obviously been reading GAF lately.
Meanwhile, I want there to be 10+ "towns" to explore across a huge map - a new land that is different from Hyrule. Each town could have dungeon-like and side-quest like activities to complete, and most of them host a difficult-to-access dungeon, requiring keys or knowledge from the town or adjacent towns.
You can venture off in any direction at the beginning of the game (you're not forced to learn anything or equip yourself in your home town), and complete the town areas in any order.
But some of them will require some things from other towns/dungeons, and the final dungeon area will require things from each dungeon to fully complete, although you can attempt to play the final dungeon to begin with if you like (you won't pass, but there's no arbitrary restriction to enter it). The final dungeon isn't the end though, it simply unlocks a pathway to a very final otherworldly location.