One wonders how there are people in Misery Mire, considering the only way to get in is via a portal that is only accessible by using the magic flute (and you're apparently the first person to have used the flute in some time, considering that the bird in Kakariko town square actually pops out of a sculpture when you play it). The story rules out the possibility that they were there before Ganon transformed the Golden Land into the Dark World, as he was apparently the first person to enter the region for an unspecified amount of time. Most likely there are other methods of entering that aren't represented by game mechanics and the MST3K Mantra should apply, but one wonders why Link would have had to go through all the trouble then.
It's feasible to believe that since people had been getting trapped in the Dark World for centuries, someone may have at some point blocked off the Mire between Ganon's imprisonment and when Agahnim weakened the barriers. It's also believable that the Sacred Realm had SOME kind of native life in it to a degree, since Ganondorf was the first being from Hyrule to enter since the Sacred Realm's creation.
As I played through The Legend of Zelda: A Link to the Past I wondered to myself, why is it that even though it was stated that the properties of the Dark World cause those who enter it to shapeshift into something that reflects their true natures, Agahnim looked exactly the same as he did in the normal world? And then I finished the game and it hit me: Agahnim is basically nothing more than a host for Ganon's spirit; he has no soul of his own, and Ganon was already changed into his boar form.
I used to think that the three pendants you have to collect (Courage, Strength, and Wisdom, respectively) had no reason for the order you gathered them in, but now they seem to be in order based on how soon Link (and by extension, the player) would gain those respective traits. Courage comes first because you need it just to start your journey. Strength follows after you have started gaining new items and powers. Wisdom comes last since Link and the player need time to master these items and become comfortable with the gameplay.
Why is it that in A Link to the Past, the Master Sword is no longer able to destroy Ganon by itself, even though in all the other games it's the only weapon that can kill him? It's not because the sword is less powerful (in fact, the Golden Sword upgrade may be the most powerful sword in the franchise). It's because Ganondorf was able to claim the entire Triforce when the Hero of Time was defeated and is at his most powerful. Even the Master Sword's enchantments against evil is unable to counter the power of the Triforce, and it takes the Incorruptible Pure Pureness of silver against evil to finish him off.
The thing is, the Master Sword was specifically forged as a failsafe in case the Triforce was used for evil. The Master Sword suppresses the Triforce's power, making the holder of the Triforce powerless. Still some Fridge Brilliance here: Ganon wasn't hosting the Triforce in his body at the time — it was in a locked room behind his chamber in the Pyramid. The Master Sword was still a sword, so it could be used for the first half. After that, Ganon used his magic to make himself invulnerable, which only Silver Arrows could undo.