How I'd make it (never gonna really happen)
Hyrule has been prosperous over a thousand or more years of relative peace. Basically no massive cataclysms. But its also corrupt and bureaucratic, magic has faded away and the other races retreated deep into their kingdoms. Wars have been fought against rebellion, pretenders to the throne and other nations of hylans/humans.
Link is a cynical thirty something guardsman-lieutenant, a minor officer who has gained his rank through merit in the field of battle, but hasn't advanced far due to a lack of political or family ties. He looks the same just grizzled and older, short cropped hair and beard, scar running down one side of his face across his eye. Hes an expert swordsman but with a brawling no rules attitude. He wears a guardsman's uniform of green with armour.
Zelda is a idealistic young princess who wants to change the world.
Suddenly the sky darkens and some cataclysmic event happens, coinciding with Gannondorf's, a rebel leader, attack on the palace and Link is part of the escort to get Zelda to safety. He would be the only one to escape alive with Zelda.
Now Zelda remembering fanciful stories of the ancient hero, the gods and the other races, decides to unite Hyrule and find a magical solution. Link is not impressed, but he is ordered to follow her and obey her every command, so he does, making sarcastic comments frequently (oh yeah he can speak). Unlike other Zeldas, you would spend a lot of time with the princess.
You would escort, protect her and do missions for her. As a gameplay mechanic she'd be a companion would heal you and eventually fight alongside you with magic.
Now the enemies would be both magical and monstrous, but also include humans brigands and desperate refugees.
Magic and other mystical stuff would be present but with an emphasis on how amazing its reappearance is, rather then being a common happenstance. As the game progressed thing would become more and more unbelievable to the characters.
Overtime Zelda would learn how much her people were suffering before the event. Link would find something to believe, eventually taking up the master sword and saving the day (way near the end). The two would also fall in love, not this first sight love from affair stuff, as initially they would hate each other, hes a crass violent commoner, shes a stuck up princess etc.
Overall still being a fantasy tale, but one of hope, love and redemption.