Umm, let me think. Yes.
I would love to have dungeons like in the original LoZ that you were never explicitly told to go to like in TP or ST. That's a big part of what made the original NES game so awesome (the exploration in general, not just the stumbling upon dungeons). If they did this in SS, I would literally eat my Minish Cap.
Not only does that add to the exploration value, it also gives a reason to check absolutely everywhere you go and that gives you reason to want to walk all over the overworld. This would easily put SS near the top of my top five Zelda games list, even though I don't really have one at the moment (I'm reevaluating my rankings, sue me).
So, in summary, that would be the single greatest thing (besides beefing up the difficulty of the game and WM+) that Shiggy and Aonuma could incorperate into SS.