Somebody mentioned natural disasters?
I've had a theory for some time now that due-north in TMC is not due-north, similar to how I beleive ALttP's "north" is more northeast, with the Master Sword being north (similar to how many old RTS show "northeast" as being due-north). Mount Crenel was a simple mountain, that eventually blew it's top and destroyed Hyrule Town and Castle. It was renamed Death Mountain in remembrance of the tragedy, and due to the damage done to the land, the Hyruleans moved west a bit (south on TMC's map), which puts Death Mountain in it's current place, removes the Veil Falls, gives us a new location for Lake Hylia, and accounts for the missing Castor Swamp and Wilds.