So here's my incredible thesis. I quite like the Legend of Zelda series, Wind Waker and Majora's Mask in particular being my all time favourite games. But I think that when you look at the official Zelda Timeline provided by Nintendo, the stories don't all match up, and they all point toward a different story than the one that the individual stories tell. Some I'm here to take a look and exaggerate a lot of points for humorous value and jump to insane conclusions.
The first thing I notice is that, from a certain point of view, Ganondorf is actually the victim. He's lived in a desert his whole life and just wanted some more land so he can be a bit safer. And why does Ganondorf and the rest of the Gerudo Tribe live in the desert? Let me back up a bit with my theory.
In Skyward Sword (Which I never finished by the way), there are the Skyloft people, who are strongly inferred to be the ancestors of the Hylians, and since there is another person ruling the surface world during that game, I can assume that he is killed by the Skyloftians, who then proceed to steal his throne. I assume that this ruler, Ghirahim, was one of the ancestors of the Gerudo tribe, and that the rest of his people were banished to the desert. Essentially my theory is that Ganon is the descendant of those people and is trying to retake the land that was originally his, meaning that the people who became the Hyrule Royal Family have always been the original aggressors.
But why would the Hylians do such a thing? Probably because at the start of Skyward Sword, they were practically commanded to by Fi, who was created by the goddesses themselves. Meaning that the very original aggressor of the attack that resulted in the events of all of the games containing Ganondorf, was actually the goddesses.
But again? Why would the goddesses do this? What is the end goal to the Hylians ruling the surface? The Hylians and Gerudo were both living in peace beforehand, so what's the point of it all? The same reason that the surface of Hyrule has a seemingly infinite amount of deathtraps containing caged animals that are disguised as worship temples. And the same reason that the topology of Hyrule randomly rearranges itself every couple of hundred years. Because the goddesses just want to watch the Links, Ganondorf, and the Hyrulian Royal family dance in the palms of their godlike hands. If the goddesses had a direct goal, they wouldn't keep resurrecting/reincarnating the main players on both sides of the conflict, unless the only thing that results from the conflict is the conflict itself.
That's why the stories and gameplay of Wind Waker and Majora's Mask seem more unique. In Wind Waker, the goddesses flooded Hyrule because Ganon appeared to have permanently won because the existing Link didn't come to defeat Ganon, so they waited for Link to reincarnate so the cycle could repeat one last time before Ganon dies permanently. And in Majora's Mask, Link is seemingly in another dimension, and therefore out of the goddesses reach, meaning that the source of the conflict is legitimate conflict between the Skull Kid and Termina.
Esentially though, what my theory boils down to. Is that the goddesses are not goddesses at all, they're just hugely powerful and incredibly bored alien entities who wanted to make some mortals dance. There might be others like them who have their own goals. In fact, the species the goddesses belong to might well be a relative of the Shinigami from Death Note, but with different powers, as Ryuk the Shinigami is also a hugely powerful and incredibly bored alien entity who wanted to watch some mortals dance.
In fact, come to think of it, we don't know for certain that the planet that Hyrule located on is actually Earth. Ocarina of Time mentions Earth once, but more in the idea of the ground beneath their feet rather than as a name for the planet. It could be that the real Earth exists somewhere else in the Zelda Universe, and Ryuk decided to play a game with the lives of mortals, after hearing of the idea from his foreign friends, Din, Farore, and Nayru.
Thanks for sticking around reader(s). Just so you know, I'm perfectly aware that I have some of my facts wrong, and this crazy theory was for my amusement only. This is still canon in my imagination though, because knowing everybody's motivations once the mystery is gone helps me to enjoy the story more. And I think that the fact that the only reason these characters exist is to provide entertainment for the player probably only adds to my theory.