This idea originally started as a joke to end an argument about a sequel to Spirit Tracks being impossible. Then, as I started to think about it, I thought that the idea seems plausible. So here it is:
CYCLIC TIMELINE
I'm actually starting to believe that Nintendo's plan is to join up the adult timeline with the birth of Hyrule, creating a cycle. What I mean is, after the end of Spirit Tracks, the Triforce is created, war between Hylia and Demise occurs, and Skyward Sword begins.
Before you dismiss my theory, listen: New Hyrule was discovered after the Old Hyrule was flooded. The Demon King Malladus shown in Spirit Tracks bares many similarities to Demise. (The fiery red hair, the horns, the yellow eyes, etc.) He also has a loyal servant, Chancellor Cole, who could be replaced later with Ghirahim, and he was sealed beneath shackles by the 'Spirits of Good' prior to Spirit Tracks. Who isn't to say he broke free again in order to steal the Triforce?
However, during Spirit Tracks, the Triforce was absent...maybe not even existent. Well, what if the Golden Goddesses returned, reincarnated as the 'Spirits of Good' and created the Triforce. There is evidence for this, as the Lokomo symbol contains a lone golden triangle in the centre of an arc. (I will not go into the Tetraforce theory.) After this, Malladus/Demise made him escape and tried to war with Hylia. Then, the events of Skyward Sword took place?
What if the seven Lokomos are reincarnations of the Seven Sages of the Master Sword? This theory makes sense, as each Lokomo also has his/her corresponding element, and Anjean gave Link the Lokomo Sword: possibly an early incarnation of the Goddess Sword?
But some of you may say that Zelda must be one of them to complete the group, as she was the Seventh Sage. Well, some people actually believe that Anjean is Tetra, hence the hairstyle, the mystery surrounding her knowledge of Zelda & Link. Also, she continuously says "Her ancestors would be proud of her", either referring to Tetra directly, or talking about herself.
Now let's look at the map of New Hyrule, in comparison to the Surface:

You will notice that the Snow Realm lies perfectly beneath the Thunderhead, which remains undiscovered in Skyward Sword. This, coincidentally, matches perfectly, as before beating the Blizzard Temple in Spirit Tracks, there is in fact a Thunderhead surrounding the temple!
Now for other locations. Looking at the neighbouring Fire Realm, I think it is safe to say that this could be a further incarnation of Death Mountain/Eldin Volcano. It is a fairly flat, actively volcanic mountain inhabited by Gorons, so the connections are easily made.
But what about the other two realms? Well, let's start with the Ocean Realm. Remember how we saw that Faron was flooded by the Water Dragon? What if it was originally an ocean, but Faron drained it to form land? What if the Ocean Realm becomes Faron Woods, and the Marine Temple becomes Faron's Spring/Ancient Cistern?
As for the Forest Realm...well, Lanayru Desert was once a grassy green plain... Over a long period of time, it dried up. So was the Forest Realm the original Lanayru Desert? Well, where is the Sand Sea? Of course, it lies to the west of the desert...which, coincidentally, is where Outset/Aboda Village and the entrance to the Dark Realm lies! In the ocean!

Or would it be more reasonable to say that the Demon Altar became the Temple of Time...
Finally, there is the case of Force Gems. In Spirit Tracks, Carben states that they are produced 'when somebody's gratitude is so powerful, it forms a crystal'. Does this sound familiar?
Of course! Gratitude Crystals!

If Force Gems are forms of Gratitude Crystals, that means that they have existed for millenia! This surely proves that the people of New Hyrule and the people o Skyloft have some sort of ability which connects them?
Now for my latest piece of evidence: Rabbits!
In Ocarina of Time, Rabbits which used to wander Hyrule Field became extinct due to poaching, hence the Poacher's Saw seen in the Biggoron Trade Quest. When you give the Bunny Hood to the Running Man, he says it reminds him of those rabbits, and wears it in an attempt to run like one. (Which is what the Bunny Hood does in Majora's Mask.)
Rabbits were never seen again after the Great Flood until the birth of New Hyrule. Rabbits were still alive and breeding here, so the Hylians could save the species. The way they did this, of course, was with the construction of Rabbits Haven. The Rabbit man states that rabbits must be kept there to 'protect them from harm'. Could this be poaching?
If the Rabbits are under threat, does that mean that in a few centuries or even decades, they will die out totally? What if this then leads on to Ocarina of Time again, and so completes the cycle?
Now onto technology. And to one person in particular:
So Beedle is first seen in Wind Waker as a humble ship merchant. He continues this trade during Phantom Hourglass. But then when we reach Spirit Tracks, we find that he has upgraded to an Air Ship. So where else do we see an Air Ship in Zelda?
Yes, all the way back to Skyward Sword. Now, I'm not in any way trying to say that this Beadle is the same Beedle. But I just feel that this jump in technology, from an Air Ship, to a Ship, to an Air Ship again, is too great to ignore. Wouldn't it be more likely if Skyward Sword happened after Spirit Tracks?
This would explain how such technology is available in Skyward Sword. And how to explain why Beedle reverted back to ships? Well, after the Great Flood, his ancestors would have to start again like everyone else.
If my theory turns out to be correct, this would change the shape of the timeline completely. It would sort of resemble a circle with a tangeant representing the child timeline veering off from the cycle. Does anybody catch my drift? Or is this all nonsense to you?
