Challenge by King Ceasar Jr:
No fourth wall breaking!
The protagonist and hero of the story has to be Link from both Legend of Zelda and Ocarina of Time and Majora's Mask. However Link has to have all the skills, strength, gear, magic and spells from all The Legend of Zelda games in the Legend of Zelda Timeline(the Nintendo games, we do not speak of the CDI Zelda Games)and has the sheer strength and combat skills that he has in Hyrule Warriors at his maximum potential so he can be an ace to hold his own against some of the strongest as well as the most evil foes in both series. However Link has to learn martial arts and hand to hand combat and be as proficient in that area of skill as he is with his weapons on the off chance he cannot cast spells or is stripped of his weapons.
Now onto the reason why Link has to be the protagonist Link would fit the Visual Novel's Prophecy of the Messenger of Heaven perfectly as Link is the chosen hero of The Gods of Hyrule and is the bearer of the Triforce of Courage. If I were you, I would go with Link's personality and character portrayal in the Ocarina of Time and the Majora's Mask Manga and see how he matures in a war and eventually in his role as a king as you write the story but still be somewhat in character with his depiction found in the Ocarina of Time and The Majora's Mask Manga.
For the adaptions of Koihime Muso, you can do whatever you want but let me lay down some guidelines so you can have a solid frame work. If you go with the Visual Novel and it's sequels or the Anime and it's subsequent seasons Link has to use his strategic know how from his adventures to his advantage on the field and him kicking ass against some of the big dogs of The Three Kingdoms. For the routes of the Koihime Muso Visual Novel and it's sequels like Shin Koihime Muso, you can do whatever you want so long as it fit's Link's character that is in the Legend of Zelda Ocarina of Time and Majora's Mask Manga as that depiction of The Hero of Time is the most believable and human like incarnation of Link and also one of the best depictions of Link to date.
If you want to go with the Anime go take a look at the Armored War God's Saga, A Kamen Rider and Koihime Muso crossover for some inspiration while also incorporating some elements of the Visual Novel's into the Anime. You can bring in monsters from the Legend of Zelda as antagonists and also some of the villains from both franchises(excluding Ganondorf as he is in a interdimensional slammer)who oppose Link. Such as the White Cloaks from Koihime Muso, who want to stop the Prophecy of The Messenger of Heaven and whomever has the title from uniting China, and some followers of Ganondorf and monsters from Hyrule who want revenge against Link for defeating their master with both factions eventually joining together to try and put an end to Link and his companions quest to unite China and save the world from the White Cloaks and Hyrule's worst.
Now for parings, seeing as Link is a Heterosexual Male and a Young Man at this point in time he has pick up a girlfriend, but the love interest cannot be not a loli and Link is not into little girls, you can pair him up with whoever you want, you can also give Link a Harem if it suits your fancy. Link has to find love, and also one day inner peace and happiness after all his adventures.