I'm okay with this too. Though -
I said size manipulation, not shape shifting. When Link takes a shrine crystal to it's location, the crystal literally grows in size. The only thing that separates the physical form of the Zoni and the Minish, are the horns and the third eye, which both have a mechanical look. The hero aspect has neither the third eye or the horns, and even has a tail with a red tip. the eye and horns are obviously body modifications.
For the Rito, we have a few additional points to consider. The legend of the Storm Ark depicts a time before the Cloud Barrier. The Skyview Temple (SS) has images of loftwings, yet the statues that are found throughout the temple more closely resemble the Rito we see now. It's also worth noting that the Rito in Wind Waker have a different physiology, requiring the aid of a dragon to mature.
For Groose, I've always thought that too, until recently. Though, on my last play through, I realized that Groose wasn't the only red head on the island. It may be, if I am right about the time placement, that the very next male Gerudo, or rather the woman Hylia knew would lead to the next male, was sent up with Skyloft, to keep him from becoming the next Ganondorf, especially during the problems with the Imprisoned/Demise. Yet, he was still drawn to that source of power.
Again, no retcon. Ganondorf is still part of the curse. Instead of the curse making Ganondorf from nowhere, He was already sealed below, and had strong ties to Demise's powers. When the curse is enacted, it latches on to Ganondorf, who is then able to trigger his own twisted resurrection. In fact, some are postulating that TotK Ganondorf was literally sent against Hyrule by his god - Demise. Then when Ganondorf failed, Demise pulled a Thanos, and decided to do it himself.
Comparing the positions of the Master Sword pedestals in BotW/TotK and SS, and the Springs of power in those games, the castle in question is out of the map, for SS. I am currently working on an update on my map theory. Keep an eye out for that.
It's literally in the prologue of the game. Hylians are Hylia's chosen people. The humans of that title have the pointed ears. The humans, chosen by Hylia, who have pointed ears, were raised to the sky, by Hylia.
And, do your research before slinging baseless insults.