The plot bunnies are working overtime tonight!!Come suffer with me if you dare.
1) Fierce Deity is Hylia's son with the first Link (First, not Sky) and he is to navigate through the new world of Skyloft. He is bullied for being an orphian and a half breed. His father died during the fight against Demise's armies, leaving him in the care of the newly built Academy. He works to be the best student to ever graduate, but he is still an outcast. He outlives everyone every generation and he leaves to the surface. Later, he hears about this Hero and his Princess and how it sounds like his parents story. He hates it. His anger is felt by his Uncle, Demise, and he is taken in by him just to be a pawn of evil, but he refuses to what is asked and is forced into the Mask. Basicly an origin story and later has to fight his mother because she has become the very enemy she had tried to save her creations from.
2) Fierce Deity was the original Link (First). He loved Hylia, worshiped her without question. She claimed to love him too, but her desire for peace, balance and order were far greater than her love for a Hylian. She told him how she would make him powerful enough to help her defeat Demise, how they could be together forever, turning him into the Fierce Deity. Seeing that it was all lies just to use him and his knowledge of the battle fields, he grew angry and broken by her and turned against her. She created the Mask and cast him away. He still loved her, but cursed her name.
3) Wild can time travel!! Think about it... when playing BOTW and TOTK, we can pause and save where we are at to go back if we need to. The screens to save and continue is on the Slate. So what if Wild is able to save the last three hours or so and just go back when something goes wrong? He could do the same as Time, but less dangerously. What if Time is the only one to know since he also time trevels and because he has an interal clock that glitches when Wild does it. Time doesn't lose his memories, just adds more and doesn't piece together any of it until something horrific happens (like a member of the Chain dies over and over again or a different one every time) and he and Wild are the only ones being traumatized by it all.
MY BRAAAIN!!!! lol