I think my favorite is 2D with Exploration. SOTN is an awesome game, but it could have been fine tuned a bit more, there was a Ton of stuff to do and find, which is both a blessing and a curse. You've got Items you use up after one use, you've got Items that use MP, you've got items that use Hearts. Hearts alone would have been fine if you ask me. Also, while I love the idea of your character getting stronger as the game progresses, It seems to me the Leveling factor allows for players to become too powerful. I think borrowing from Zelda, and making Life up and Magic ups, along with various weapon, armor and accessory options/upgrades the main way to strengthen you character, and balance the enemies appropriately.
I'd also like to see more of the world out side the castle, much like we got in Simon's Quest, Doing so would allow for more logical shop set-ups (Unlike the Librarian or Hammer.) I must admit though, the most recent game I've played is Dawn of Sorrow, I know this has been addressed in more recent games... I just haven't had the chance to try it out yet.