Essentially, this proposition suggests that we should ignore the map of Hyrule from Ocarina of Time and should instead use the map from Twilight Princess when discussing the possibilities of geographical evolution in Hyrule. The main reason behind this is that the maps are fundamentally the same. In the past, both recent and distant, there have been theories which use connective lines to show relative location. By using lines to connect two locations, such as Death Mountain and the southwestern desert, which are two common regions seen in many Zelda games, you end up seeing that they are positioned relatively the same from game to game. If you use the easternmost peak of Death Mountain (if two peaks are present) as your first reference point and about the middle of the desert as your other reference point, and connect them with a line, you will see that it either cuts a straight through Hyrule Castle or ends up coming close to the southeastern corner of the immediate area. If you then compare this line to a line constructed in the same fashion on a different map, you will see that they are about the same length and often at similar angles.
This is pretty much the case with the maps of Hyrule from Ocarina of Time and Twilight Princess. Drawing a line from Death Mountain to the deserts on both maps shows that, relatively speaking, they are in the same location. Despite the fact that Death Mountain has a placement more to the east in Twilight Princess, it is still aligned horizontally with Hyrule Castle as in Ocarina of Time and a similar distance in some northeastern direction of the desert. Although the angle between Death Mountain and the deserts do not match up between the two maps, a logical explanation can be found for this predicament.
The angles between Death Mountain and the deserts do not match up is because in the map of Twilight Princess, we are not shown the actual peak of Death Mountain. From the field, you can see a massive, blister-like rock formation rising in the east, which is apparently oozing lava through cracks in the surface. This appears to be the actual Death Mountain, and judging by the looks, it is befitting of the name. Apparently, Death Mountain is not only the name of the mountain itself, but also the range of mountains in the surrounding area. In fact, this was the case in the original Legend of Zelda. We do not actually go up on the true Death Mountain, which is shown by the fact that you can see the massive sphere of rock and lava looming over the landscape from any part of the mountain accessed in the game. Knowing this, if we were to determine the approximate location of the actual Death Mountain on the map of Hyrule and draw a line from it to the Gerudo Desert, it would certainly match up more closely with the line on the map of Hyrule from Ocarina of Time than when the line was extending from the lower reaches of the Death Mountain range.
Instead of a complete retcon of Hyrule, which you may have understood this article vouching for earlier, a combination of the two maps should be taken into consideration. The reason for this is that any areas from Ocarina of Time can easily be placed on the map of Twilight Princess without much effort or conflict because of how similar they really are. Basically, you can think of taking two maps at the same scale from each game and cutting out certain areas from Ocarina of Time's map and placing them on the map from Twilight Princess in about the same areas they belong. In doing so, it isn't so much of a retcon of all of Hyrule as it is simply redefining the central areas while leaving the outer territories intact.
Let's take a look at an example. Standing atop the Gerudo Mesa in Twilight Princes, take a look around, you will see much more desert, completely inaccessible, extending all the way out to the horizon. It is very possible that we are being shown only a part of the desert southwest of Hyrule in Twilight Princess, this part being called the Gerudo Desert.
What this means is that the desert and surrounding area from Ocarina of Time, known as the Haunted Wasteland and Gerudo Valley, are located somewhere else nearby. Remember the conversation in Twilight Princess that Link had with Auru about the desert, shortly before Fyer launched you from his cannon? Auru spoke of a path to the desert which had been lost long ago. Perhaps this path was the Gerudo Valley? Seeing as Bulblins have such an easy time destroying massive stalactites with bomb arrows during your trip up Zora's River in Twilight Princess, it seems evident that much of Hyrule lies on relatively soft rock. Taking into consideration this weakness, it is possible that the Gerudo Canyon collapsed in on itself or had become impassable in some other similar way. Another thing from Twilight Princess tells us that this is fairly likely to occur. Just south of Hyrule Castle in Twilight Princess, there is a gaping hole high above Zora's River. Evidently, after years of erosion, and perhaps some outside influence, this patch of ground suddenly gave way. Knowing of this other instance makes the theory that the Gerudo Canyon fell in on itself more plausible.
The question now is, where was this ancient pass, the Gerudo Valley, located? In Ocarina of Time, there was a massive cliff facing the Gerudo Fortress from the south. In Twilight Princess, there is a large number of massive rock formations, and apparently a large stone cliff, located around and behind the Arbiter's Grounds and the accompanying Mirror Chamber. This rocky area is located in the northern part of the Gerudo Desert. What this article suggests is that the area surrounding the Coloseum structure of the Arbiter's Grounds is located a relatively short distance south of the Gerudo Fortress. Now, one could argue against this by saying that you cannot see any such structure, nor any other rock formations, behind this cliff if you climb up to a high point of the Gerudo Fortress and look towards the south. Taking into account that Ocarina of Time was developed nine years prior to Twilight Princess, the developers probably had not thought of placing such a thing in the desert, and had no need of any such thing in the game, so they didn't waste time and memory space to make it and place it there. Over time, creators change their minds and decide to go in new directions and add new things to their work, so perhaps one such thing was a structure close to the Gerudo Fortress which closely resembles the Roman Coloseum of our world.
Let us now ask ourselves why such a thing would be positioned there. Of all the places that a prison could have been built in the desert, it had to be located near the Gerudo Fortress. Well, let's look at things another way. We see that in Twilight Princess, the Arbiter's Grounds are an absolute mess. Buildings are in ruin, and are slowly being swallowed by the infinite sands of the desert. However, in Ocarina of Time, the Gerudo Fortress looks practically brand new. For all we know, they could've laid the last sun-baked mud brick a few days before Link stepped foot in the Gerudo Valley. Perhaps it was not the Arbiter's Grounds which was built near the Gerudo Fortress, but the Gerudo Fortress which was built near the derelict Arbiter's Grounds. Proof of this involves looking at some other architecture in Hyrule. Located upon a cliff just northeast of Lake Hylia in Twilight Princess, there lies an ancient stone structure reminiscent of the amphitheaters of the ancient Romans from our world. Seeing as both this amphitheater and the Mirror Chamber display traits typical of Roman architecture, we can conclude that they were constructed during a similar time period. The two, however, are in completely different conditions. The amphitheater is in ruin, and the Mirror Chamber is largely intact. Knowing Hyrule has had a violent history, it is possible that the amphitheater suffered from attacks, whereas the Mirror Chamber remained isolated in the Gerudo Desert.
Now that we have answered the where and why, let us look to the how. How are the Gerudo Desert, Haunted Wasteland, and Gerudo Valley positioned in relation to one another? Let's look at the shapes of the two and how they relate to Lake Hylia, which has essentially the same shape along the western edge in both maps. If you look at the shape of the Haunted Wasteland and Gerudo Valley from Ocarina of Time, you see that they form a 'P' shape with a funny little tail, Gerudo Valley, coming off the bottom of the circular section, the Gerudo Fortress, with a large space between it and Lake Hylia. Looking at the Gerudo Desert from Twilight Princess, you see that it has a roughly triangular shape, with the bottom right corner taking the shape of the nearby Lake Hylia. Taking into consideration that the two maps may not be at the same scale, and in all probability aren't, then it's entirely possible for the Haunted Wasteland and the Gerudo Valley from Ocarina of Time to arc around the Gerudo Desert without any major complications. The ancient entrance to the desert which Auru spoke of would then be located somewhere around the rocky cliffs in the northwestern part of Hyrule Field seen in Twilight Princess.
The next example is the matter of the southern forests. If one compares the two maps, it become apparent that they both have wooded areas towards the south. Twilight Princess has the Faron Woods along the southern border of Hyrule Field, and Ocarina of Time has the Kokiri Forest and Lost Woods extending northeast from the southeast corner of the field. What is significant here is that on both maps there is empty space in the location the forest from the other map would occupy. Again, with appropriate scaling and minimal rotation, the two forests could be brought together on the same map to form a more complete forest along the southern border of Hyrule.
This somewhat goes along with the "comlete forest" comment. The Hyrule we are shown in Twilight Princess more closely fits the romantic descriptions we are given in many games; a land surrounded by tall mountains, encircled by lush forests, and filled with fertile fields. It seems rather obvious that the development team for Twilight Princess wanted to strengthen this description of Hyrule and show the land in the way it was meant to be seen for the past twenty years. Obvious, because the developers gave us two large mountains to explore and the many other mountains seen on the edges of places within our reach. Obvious, because of the extensive forests we find ourselves wandering through and seeing up above us on cliffs. Obvious, because of the great amount of detail put into the places we can see but can never get to, no matter how much we want to. As of late, the developers have been putting great amounts of effort into returning the franchise to its golden era, a time during which you could have been considered cool for slaying a foul beast and rescuing the princess.
Knowing the developers have been putting forth such effort, I feel that we must cease to cling to such old ideas and interpretations of things, such as geography. The way I see it, the developers decided on the split timeline because it gives them the freedom to reinvent the series without greatly affecting the work that had been done in the past. Twilight Princess was just the first step in this process of rebirth, so we should focus more on the present state of mind of the developers and not what they have said or done in the past. Being a timeline theorist isn't about looking at the things characters say or how the world is arranged anymore. We now have to take into consideration an additional factor, the human factor. The creators of the Zelda games care greatly for their creation, which can only be described as art, so they will change things in ways that they feel will benefit the franchise. To fully understand the way the timeline is to work, we must not only look at things from a perspective based solely upon logic, but must place ourselves in the shoes of people like Miyamoto and Aonuma. By understanding them, we can understand their work, and we can understand the timeline.