Before the village was transformed into what it is in OoT, the well could have served as an entrance to a prison, like you guys have said. Who knew what that village could have looked like prior to Impa turning it into a place for the lost and homeless.

To me, the temple portrayed the dark part of Hyrule. A constant reminder of the sins committed throughout time in their pursuit of power and control.

Hyrule did have a war, that much we know. It could have been a war between two races, or a war with another part of the world, or a civil war.

"here lies the bloody history of hyrule's greed"

This quote: For all we know, Hyrule could have been responsible for the war rather than just defending it. Maybe the king wanted to expand the country and went out too far and invaded the wrong lands. In his lust for power, he caused many deaths.

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"What are you doing here, you little weirdo?" - Ingo to Link, Ocarina of Time.