If you think about it this way, then maybe some light will put on the subject(or whatever).
Ocarina is the splitting of the timeline, as you said.
Timeline A: In ALttP, Ganon converts the Golden Land to the Dark World. Aghanim brings him back with Zelda's unwilling help. This would happen after Majora's Mask.
MAYBE ALttP's Link's father is OoT Link. He has the shield, he has a sword, and apparently he's highly trained because he goes after Aghanim by himself.
Twilight Princess starts Timeline B, like you said. Ganon is still in the Golden Land, converts it the the Shadow World(or whatever it's called) and escapes through Zant. Somehow, a new Link appears, defeats him. And the story continues.
Why do I say this? One simple reason: Kakariko Village. I only remember OoT, Majora's Mask, ALttP, and Minish Cap. But, I don't think that any other game has Kakariko Village. So, I believe that Kakariko Village is the key. If I'm mistaken, please tell me, I don't want to be mistaken in this.
Another theory that I have is that Twilight Princess, OoT, and ALttP arer the same story, retold over the ages.
