Twilight Princess
was originally going to have magic, but then they took it out for some reason. The box art for
TP features a magic meter, in the screenshot where Link is fighting a darknut:
You can check your own
TP boxes (Wii) to confirm this.
I wonder why they took it out.

In the screenshot, some of the magic has been used up-- I wonder what it was used for?
Anyway, I hope the next Zelda game has magic in it. I don't see why it wouldn't.
TWW even had a primative alchemy system (Chu Jelly, etc.) which was cool.
EDIT: The screenshot only appears on the Wii box art.