I'd definitely like to have her be a companion on the journey like she was in ST. Although part me would like her to be a fully playable companion in the game, sort of like the duo in Ico, I'm not sure the devs would have an easy time pulling this off without it being overly cumbersome. She would need some seriously good AI and the whole game would have to be based around companion mechanics. Maybe an easier way to go would be to temporarily have her join in during certain more structured parts of gameplay, such as the leadup to dungeons, or even in dungeons themselves.
Or she could be something of a spirit companion again. If this was the case she could be the source of Links rune-like abilities this time, perhaps starting with several magic powers, one for each of the three Goddesses and maybe even a fourth one as the descendant of Hylia (possibly being able to acquire more powers through the course of the game). This way Link would be the fighter, and Zelda would essentially be the puzzle solver.