Game Engine Mechanics
The map will scroll with the player (a la Pokemon, not like Zelda: Link's Awakening) but will allow freedom of movement not locked to a grid (a la Zelda: LA, not like Pokemon). The view will be top-down. The camera should be displaying more info in front of the camera, so the player character will be offset.
The world will be split up into large "rooms", maybe 250/250 tiles? Not sure yet. Each room will have a tileset preloaded into VRam. The map data itself will be laid out in rows in the ROM.
Doors and other special tiles
Have header/footer data in with the background map data. I'm not sure if there's going to be trap tiles, but there will be "warp" tiles, such as doors.
A day/night cycle might be a little over the top, especially on a DMG. I'm not ruling it out, but further investigation might be warranted.