I'm thinking Minish Cap style rooms, oddly shaped overworld peices, but roughly rectangular in total shape. I'm not dividing the areas like in LA, and the lagging of tile-loading doesn't matter to me much. I think I may have found a solution, using a room / area grid and X-Y room names. I'm going to put it into work sometime today, or at least test it, but I have school in half an hour, and I gotta get ready. Anyways, gentlemen, thanks for the help, I will get back on how my idea works.
(Edit):
What I set up was a grid type system. I don't really like it, but it almost worked. In a 3x3 set of rooms, all the same size(Square) (Which won't be how it is in the real thing) and all lined up, the bottom left room is ForestRoom_"X0Y0". Above it is ForestRoom_"X0Y1" and to it's left is ForestRoom_"X1Y0". When you intersect the upper boundery(If Link's Y is higher than his X in the room(Note, I know this wont work with non square rooms, but bear with me)), you will go to ForestRoom_"X0Y1". The grid continues till X3Y3. By determining Link's relation in terms of the bounderies of the room, then it can decide which room to go to. Several problems occured though.
A. The size. In the real game, I plan for the overworld rooms, IE, Kokiri Forest, Lake Hylia, etc, to be one room. Also, they will not all be square either, so the X-Y position factor will not work in the way it does here.
B. What happens when ForestRoom_"X3Y3"'s northern edge is MountainRoom_X2Y0? The whole system gets messed up.
C. When there are more than one exit on a side. It would have to determine Link's X and Y in relation to the boundary, but then, if Link's X(Going Up) was less than the X of the right door, then it would go left, and vice versa.
It seems to work in theory, I have yet to put it into code though. I see many flaws, but it's the only way I can see to start off.