Time is pretty static in the Zelda series though. How many times in Ocarina do you jump back and forth between being an adult and a child, memories intact, even to the point of changing the future by going to the past? It's that game's version of Light World/Dark World and I don't think it was meant to be taken that seriously.
If so...then there are THOUSANDS of new timelines. What about the timeline where Link doesn't plant all the magic beans? :P
So, there's a future with no Link. Does that mean Ganondorf is free to rule in this alternate timeline instead of being banished away? I'm guessing that's how they explain Wind Waker, right? Dude, he was sealed away like before. He can't return until the next 100 years or whatever. At that moment, there'd be another one of Link's descendants waiting for him. Regardless of timeline.
Or in the case of Wind Waker. Not. That would have had to have been a failure of a Link between Ocarina/Majora and Wind Waker, assuming the games are tied and that Wind Waker's events are next in the sequence. 100 Years of Darkness, do not pass go, do not collect 200 rupees.
It also doesn't seem too wise of Zelda to send Link back just so Ganondorf could go cause havoc again. She must have had some confidence he wouldn't be back for at least a little while.
Also, this is fun, I haven't geeked out in a while :P
edit: Yeah! Branches!
Wrong, wrong, wrong.
I used to think this as well, but then I started posting on Zelda Universe and I got a serious new look at things.
Basically, in all of the situations where Link changes the future, he RETURNS to the future to see those changes, whereas at the end of OoT, he returns to childhood forever. This is what creates the split. Because Link does not go back to the future, the changes he made are not applied to the future, creating two separate timelines.
ALSO for reference: Nintendo's OFFICIAL timeline: (http://www.zeldadungeon.net/wp-content/uploads/2011/12/Hyrule-Historia-Timeline-translated-Graphics1.jpg)
Except, some of the games had continuity to begin with. Link's Awakening was the sequel to ALttP. OoT and Majora's Mask are directly connected BY TIMELINE CHANGES. Oracle of Ages/Seasons are connected. Wind Waker, Phantom Hourglass and Spirit Tracks are all directly connected.
Point is, you are fooling yourself if you want to deny a timeline with multiple routes exist.
This basically.
Plus Miyamoto did state that he had an official timeline LOOOOONG before the Hyrule Historia came out, and he just didn't intend to release it.
Partners in Time storyline theory.
Spoilered because spoilers derp.
In the game's prologue, it said that the Shroobs invaded the Mushroom Kingdom, attacked everyone in the past, and forced the infant-version of the protagonists out of the castle. This was all way before E. Gadd invented the time machine that took Princess Peach and two of the Toad assistances back to the very time the Shroob Invasion began. Back in time, Princess Peach used the Cobalt Star (the source of power used for the time machine) to seal away the Elder Princess Shroob then she, and the Toad assistants, were captured by the Princess Shroob's sister. The time machine returned to the present, badly damaged, due to the curiosity of the Junior Shrooboid (the game's first second boss) This was when the titular characters and the others learned about the Shroobs. Then begins the main game.
Now, as for the theory:
My theory is that since the Shroob Invasion happened in the past a major event had to happen in which either the protagonists or the Shroobs lost. If the Shroobs won, than Mario Luigi, Princess Peach, Bowser, Toadsworth, and more than half of the entire Toad population (due to harvesting their Vim for the Swiggler to power the Shroob's UFOs) wouldn't exist in the present...as they are portrayed now. So, since the previously mentioned characters are still alive, a heroic event happened that the Shroobs lost to in the time between the start of the Shroob Invasion in the past and before E. Gadd's time machine was utilized in the present to get to said past. As to what the event was, no one knows. When Princess Peach entered into the past, it created a sort of...I shouldn't say "paradox," when she was brought into the middle of the invasion. The present isn't affected by this due to the Bros' destiny to go back in time and stop the Shroob Invasion themselves and rescue the captives. So, to put it simply, my theory is that none of the events portrayed in Partners in Time wouldn't have happened if Princess Peach, or anyone in the room at the time, didn't use the time machine. The only thing about the game that puzzles me is that if the events in the past happened, and if it was before Princess Peach went back in time, why didn't anyone have a memory of the Shroob Invasion if they somehow survived it and won the battle against the Shrooms?