It seems people were simultaneously right about how Ocarina of Time and how it split the timeline, and simultaneously wrong about it in a way they never could have possibly guessed. The 25th anniversary puts the order leading up to Ocarina as: Skyward Sword, Minish Cap, Four Swords, Ocarina of Time. Afterwards it has 3 branch of points, two of which are pretty much exactly what gamers always predicted. However, it's the new information that makes it all finally make so much more sense.
After link defeated Gannon at the end of Ocarina of Time he gets sent back in time, but time in that timeline continues going forward and it's that the "Hero of Time" Link is not there when that Ganon breaks back out of his sealing which causes the Goddesses to flood Hyrule in an effort to stop him. This leads into the events of Windwaker, afterwhich takes place Phantom Hourglass and Spirit Tracks.
The Link from the end of Ocarina of Time that got sent back in time told a young Zelda what Ganon was planning and four court hylian sages, different from the 7 sages of Ocarina of Time, seal Gannon up in the Twilight Realm before most of the events of Ocarina of Time ever happen. Then this Link gets sidetracked into an alternate dimension adventure in Majora's Mask. Much later Ganon would return from the Twilight Realm in Twilight Princess. Sometime after both of these events would occur Four Swords Adventures (Which has a different plot from Four Swords).
Now comes the part no one could have ever possibly expected. In alternate set of events, Link gets to the end of Ocarina of Time AND GANNON KILLS HIM. After this various armies raise up and fight against Gannon in a century of conflict until they eventually help the the seven sages seal away Gannon in the Golden Ream (possibly not the same 7 sages, thus explaining the race issue some people have always noticed), as explained in the opening events of A Link to the Past. After the Hero of LttP kicks Gannon's ass in the Golden Realm, he goes on a series of adventures which first include the Oracle Games and eventually ends with Link's Awakening. Later a different Link would get wrapped up in the Incidents of Zelda 1 and 2 (with 1 ending with Gannon flat out losing the Triforce of power at its end).
THE VAGRANT'S TALE (CREATESPACE): https://www.createspace.com/3627225
THE VAGRANT'S TALE (AMAZON): http://www.amazon.com/Vagrants-Tale-Clovis-Dye-Jr/dp/1463735359/