In the beginning there was The Legend of Zelda, and it was good. Then there came the direct sequel, Zelda II: The Adventure of Link, and it was also good if a little flawed. That was almost followed by a proper Zelda III, but it was reworked before release into a prequel subtitled A Link To The Past. Link's Awakening followed that, but all of the above were preceded by Ocarina of Time which was followed by Majora's Mask. This is about the point in history where you needed a flow chart to follow the chronicles of Hyrule, and while the creators at Nintendo eventually set the timeline issue straight, not everyone agrees on it. Over at Poison Mushroom, David Oxford tries to bring order to chaos.
This period between The Wind Waker and Twilight Princess is when I remember things going straight to Hell with regards to any sort of timeline discussion, because prior to this, there really wasn’t a discussion. There were six games with a clear linear narrative and their two bastard offspring cousins that we let hang around because they were cool, even though no one was really sure if they fit in.
Oh yeah, and among other things, Nintendo eventually thought “Hey, you know what we need? We need to go back to the beginning of the whole story!” and gave us Skyward Sword… which also had a manga prequel set before its time (and don’t believe for a second they won’t go further back; I’m just waiting for the tech in Skyward Sword to be their way of saying “it was Earth all along!“).
I stopped trying to follow the overall Zelda timeline years ago. There's no grand vision here, no meticulously planned narrative that is designed to seamlessly span dozens of entries. It's less Marvel Cinematic Universe and more LOST. Nintendo's developers are extremely talented, but when it comes to Zelda games, they are clearly making it up as they go along. There's nothing wrong with that approach.
I've come to see each Zelda title as a single adventure that may throw in some fun nods to other games in the series, but that's as far as I'm comfortable reading into details and looking for deeper meanings. Yes, Wind Waker ties directly back to Ocarina of Time, but I don't believe for a moment that Nintendo planned to eventually flood all of Hyrule when they were setting up Link's time travel escapades. Sure, Skyward Sword is the beginning of the Zelda story, but only until Nintendo releases some future sequel which is actually a prequel to that game (see also: the endless expansions of the Castlevania timeline in the early 2000s). It's unwise to look for everlasting concrete meaning where there is not intended to be much, if any at all. As soon as you reach a point where you have to say "this is where the timeline splits", you have complicated events beyond ease of explanation. Just sit back and enjoy the ride. It's more fun that way.