Reasons for why the Miyamoto order was correct at the time:
If aLttP comes in between OoT and LoZ, as many here suggest, there are several issues.
1: The AoL backstory about the Sleeping Zelda no longer works. In the context of OoT-aLttP-LoZ-AoL, the Sleeping Zelda wouldn't be the first Zelda. This makes the Naming Tradition useless, and directly contradicts the Japanese which calls her the First Generation Zelda.
2: Ocarina of Time does
not progress into aLttP correctly. OoT ends with Ganon holding one Triforce piece, and aLttP starts with him holding all three.
3: The Script Writer for OoT specifically stated that the Sages of OoT were given their names to show that it took place before AoL. If aLttP came in between the games, it wouldn't make any sense, as the Sage names aren't remembered in aLttP, but are in AoL.
4: As the primary director and producer of the series, as well its creator, a quote by Miyamoto is to be taken seriously. The quote was straightforward, and said after all the games which he was discussing were released.
So what are the problems with OoT-LoZ-AoL-aLttP?
There's really only one: Resolving the Seal War.
The Script Writer for Ocarina of Time also stated that the game was designed as the Seal War, and the character designer concurred. Thus, Ocarina of Time (at least in 1998) was the Seal War. So why then does Miyamoto not have the two games next to each other? I shall explain.
The Seal War was originally implied to not have a Hero. This story, of course, first appeared in the game aLttP which was directed by Takashi Tezuka.
Mr Tezuka directed, produced, or wrote the plot for
all of the games we have discussed to this point. He still does these things to this day, and has actually been more influential than even Eiji Aonuma, second only to Shigeru Miyamoto.
Now, when BS: LoZ came out, Takashi Tezuka was put in charge of supervising the project. I know most of you don't consider that game canon, but here me out.
I too, don't consider the in-game facts of the game to be canon, as it's just a re-telling of the original LoZ. However, the game's intro, instead of telling the usual LoZ intro (Ganon invaded Hyrule and store the Triforce of Pwer) the game says that the stage for the original LoZ is
the Seal War.
Now regardless of whether you consider the game canon or not, the man who did the most work with the game also had a major hand in inventing the Seal War story. So why would he place a remake of LoZ directly after the Seal War? The reasoning is simple: Tezuka wanted to show that, while the Seal War has to come before aLttP, it comes
directly before LoZ.
This also shows that, in the mind of the man who created the Seal War, the intent had changed, and Ganon was only intended to have acquire one Triforce piece during the Seal War, as the Seal War sets the stage for LoZ, and in LoZ, Ganon only has the Triforce of Power.
Then, in 1998, Ocarina of Time is made, and again Tezuka is given the job of Supervisor. Ocarina of Time is stated by several NoJ employees to be the Seal War, but, just like BS: LoZ implies, Ganon only gets one Triforce piece.
This wasn't a mistake. This is proof of change in developer intent. Tezuka and the other writers decided to slightly change the details of the Seal War to involve Hero limiting Ganon to only one Triforce piece.
So if BS: LoZ was right in stating that Ganon only got one Triforce piece in the Seal War, then why wouldn't it be right in stating that the Seal War comes even before LoZ?
Director intent from Miyamoto and Tezuka heavily, heavily, implies that the Seal War was not meant to
directly lead into LoZ.
Consider with me the LoZ Backstory:
LoZ original backstory said:
One day, the Great Demon King Ganon, who planned to rule the world with darkness and fear, led an evil army corps and invaded the kingdom and snatched the Triforce of Power.
Believe it or not, even though we know OoT tells the story of the Seal War, because of the Seal cast in it's ending, it also tells the LoZ backstory.
In OoT, Ganon is known as the Great Demon King, just as he is in the LoZ backstory.
In OoT, Ganon leads an army in (the soldiers say they tried to fight of his men unsuccessfully, showing he was not alone) to Hyrule, just as he did in the LoZ backstory.
In OoT, he stole the Triforce of Power, just as he did in the LoZ backstory.
While obviously the Seal cast at the end of the game is the fullfillment of the Seal War, its story goes hand in hand with the LoZ backstory.
This shows that, as the aLttP manual implies, the Ganon "born" when he touched the Triforce is the very same Ganon who attacked Hyrule in LoZ, before aLttP.
Most of this is stated in my article:
Exploring the Miyamoto Timeline
*awaits the angry mob*