You guys.... I'm really disappointed that nobody suggested the lovely Eimear Noone. Shame on you all!
Eimear Noone is popularly known as the conductor for the Symphony of the Goddesses tours, but she's also a composer... a very, very talented one. I think that Eimear, who loves the Zelda series and can truly grasp and appreciate its music, would be a perfect fit. I love Koji Kondo's work and I never want him to go away, but he won't be around forever. Plus, he doesn't do all the music himself anymore anyway. Pay attention to the credits, and you'll find other skilled composers listed.
Anyway... EIMEAR NOONE! She's talented, she's familiar with the series, and she's also married to Craig Stuart Garfinkle who is a successful film and game composer as well. So, she'd be able to share her ideas at home- an opportunity few others that position have.