I may be on to something here. In Skyward Sword, Impa states that the Master Sword is required to open a Time Gate--and as we all remember from Ocarina of Time, the same blade is needed to travel along the 'river of time.'

But the problem is... Link can only time travel in OOT at the Temple of Time, and Time Gates can't exactly be moved. So where in Skyward Sword is the Temple of Time eventually built?

This is where some of you may begin to question my theory. Many geography theorists have pondered that a section of Lanayru Desert regrows and becomes prosperous by the time Twilight Princess occurs-- to become the new site of Hyrule Castle Town.

I theorize that this section of the desert that gets rejuvinated is where the Temple of Time in Skyward Sword is! It is the location of a Time Gate, and is considered to be a sacred spot to most Hyruleans. So why not build the new Castle Town here? It's perfect.

But the problem is, that's not where Castle Town is located during OOT. It makes perfect sense for Twilight Princess, and many other theories can confirm that.

So where is the Temple of Time in OOT? The Sacred Grounds. It is the only other Time Gate location in Skyward Sword--and it is near where Lake Hylia is suspected to be in OOT. Derp.