You're welcome! A Link to the Past is missing some of the elements that you discussed such as NPCs in dungeons (I can only think of one example) but excels in terms of interactivity with the outside world. Skull Woods (dark world #3) is the best example but Turtle Rock (dark world #7) has a cool...
I like your ideas. You used Legend of Zelda as your example primarily, but I think A Link to the Past did the best incorporating the overworld environment into dungeons. Skull Woods is the obvious example, but there were other dungeons that had some additional exits like Turtle Rock and the...