I think it should be like ALttP where there is a lot of dungeons but make them harder. I think the perfect Zelda formula would be
Dungeon 1, 2 and 3 - to get things started.
D4- Midpoint- you get Master Sword/point of the game(goal)
D5, 6, 7, 8, 9, 10 - Collect things to get to said goal(Medals/pieces of Triforce/whatever).
D11 - Almost there, here is the point where you get the Final Dungeon's location, could be a dungeon where you refight all the other bosses
D12 - IT'S A TRAP - Im sorry but your Final Boss is in another castle.
D13 - Short dungeon- Maybe a straight walk to the Final Boss' lair, could be joint with D12