As the others have mentioned, yes, we've seen Zelda as a companion in Spirit Tracks. However, her helpfulness was very limited physically, and, for most of the game, only existed in the Tower of Spirits.
I would really like to see her usefulness expanded upon by her being a companion that can be present most of the time and be able to actually fight alongside Link. She would likely have a different attack set, consisting primarily of magic. She could both use damage-inflicting spells and give Link status boosts. Actually, by this point, I'm starting to think that this would be a bit overpowered, especially if Zelda is present most of the time...
Well then, I guess the Spirit Tracks model worked well, as she could only physically help some of the time. If she is to be a companion in future games, then I think following the style f Spirit Tracks would work best.