So how much do we believe there are two timelines with two different playable Links?
This is how I think it will go down. Just one playable Link.
Malice corrupts Link's hand when he accidentally releases Ganondorf by entering his sealing chamber.
The power that has bound Ganondorf over the ages had been slowly waning, and he took advantage of their visit to his chamber to escape. A mini earthquake disrupted the cavern and caused Zelda and Link to fall. The hand chose to save them and break the seal, knowing that it’s power would soon run out otherwise.
The spirit (Hand) that sealed Ganondorf thousands of years ago is thus freed. This spirit becomes a companion to Link but doesn't merge with him instantly as we saw in E3 2019 trailer.
The hand agrees to aid Link on his journey. Link's hand is corrupted with Malice and the spirit fuses with Link to seal the corruption in his right hand to stop/delay it from spreading. This means that he can no longer wield the Master Sword.
The Spectral Hand contains the Malice within the gold symbols/jewellery on Link's right hand. This gives Link new powers but he still can't touch the Master Sword as there is an ancient evil embedded in his body. (Maybe Ganondorf steals the sword)
Link then must go on a journey to the skies, guided by the Hand Companion - where they visit sacred sites of a lost civilisation to revive the Hand's power and to eventually free Link of the corruption that is spreading from his arm to other parts of his body.
Link's new ancient outfit is a result of the first ceremony in the sky - we do not see an ancient hero.
As Ganondorf's power grows on the surface, the corruption in Link's arm is strengthened and spreads to his face and chest, disfiguring him and causing an internal struggle.
When the Malice is eventually cleansed, he can once more hold the Master sword - but the spirit will remain merged with his arm.
Zelda falls into the underworld at the beginning. From there, she embarks on a series of underground challenges which releases further islands into the sky - changing the landscape of Hyrule and expanding the scope of Link's journey in the skies.
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It is revealed that the Sheikah tech had been powered by converting Malice to Sheikah energy using magic from the Zonai. This explains why Malice was continuously drawn out of Ganondorf’s body by the green magic, and up into the structure above. This deal had been going on for thousands of years, but the people of Hyrule had forgotten what the source of the energy was. This is why the tech fails at the beginning of the game. Zombie Ganondorf was essentially a giant battery. Calamity Ganon was Ganondorf taking advantage of this situation from his sealing chamber, infecting tech with unpurified malice.
The Zonai will play a role, perhaps living as an alternative civilisation underground. Maybe they will help Link to learn more about Ganondorf and how he can be killed/sealed.
The main map might be disfigured by Malice and turned into more of a horror-themed area. Perhaps there will be a heaven-above/hell-below theme.
Maybe Link will visit skies, seas, underwater, Minish etc while Zelda goes through different worlds below. They work together to affect the surface and grow in strength and gain new powers. Hopefully there will be an ongoing mystery that is put together piece-by-piece.