I think it would be three timelines.
Minish Cap>Ocarina of Time>Majora's Mask>Twilight Princess
Minish Cap>Ocarina of Time>Windwaker>Phantom Hourglass
Minish Cap>Ocarina of Time>Four Swords>A Link to the Past>Links Awakening>Zelda 1>Adventure of Link
I remember when Link to the Past came out it was clearly a prequel to the first game. Even more than that, though, when Ocarina came out it was clearly a prequel to A Link to the Past. Throughout Link to the Past you are reminded the guy you have to fight is Ganon, banished to the Golden Land, which he made into the Dark World. Later, you're told he was originally a thief named Ganondorf that was transformed by the Golden Power into the monster Ganon.
Fast forward to Ocarina. You meet Ganondorf. You fight him, you think you kill him, but he's not dead. Instead, he transforms into the beast Ganon. You still cannot beat him, so he is banished to the Golden Land (important fact: NOT the Twilight Realm. Hence different timeline). It all is set up perfectly to lead into Link to the Past. There's even seven sages that banished Ganon, leading to the seven maidens that need to be saved in Link to the Past.
Nintendo started jumbling things when Wind Waker came out and was clearly a sequel to Ocarina. Twilight Princess of course only muddles things even more.
But Minish Cap is most definitely the origin of the hero, while Ocarina is the origin of the great evil (Ganon). From there it splinters, which is fine. I like better what was once said--that it's what it says in the title, a legend. There's a legend that repeats itself throughout history of a great evil that sweeps the land, a princess that sees the land be taken to the brink, and a hero that rises up to save the day.
My consoles and the fates they suffered:
Atari 7800 (Sold), Intellivision (Thrown out), Gameboy (Lost), Super Nintendo (Stolen), Super Nintendo (2nd copy) (Thrown out by mother), Nintendo 64 (Still own), Super Nintendo (3rd copy) (Still own), Wii (Sold)
A more detailed history appears on my profile.







