This was done in a lesser capacity with Sahasrahla and Zelda in A Link to the Past and Ulrira in Link's Awakening, although in both cases there was minimal or zero character development at least from the side of the partner or helper mechanic and both games had long-distance communication (telepathy and telephone), so it's certainly not exactly what you're referring to. Just pointing out that these characters ARE human.
However Phantom Hourglass comes pretty close to what you describe. Linebeck isn't physically involved in more of your direct adventuring, but he does pilot the ship you use to go everywhere and he has character development throughout the game culminating in major changes to his character before the end. Not a lot of people cite this as a strength of Phantom Hourglass but it was one of my favorite parts of the game, personally.
Of course just because it's been done before doesn't mean it can't be done again and it would definitely be cool to see again, including in Zelda Wii U. I guess my only concerns would be these two:
1. It shouldn't be restrictive. Having a live companion with their own goals and desires is way more liable to become a restriction on the player than something like a fairy or a form of long-distance communication like we're used to. It's more likely to be the kind of thing that won't feel quite right outside of special situations -- scripted ones, mostly part of the main plot -- and the game would probably be designed to lead you toward these.
2. The companions shouldn't be too talkative in the wrong situations and dialogue needs to be good. It's the big thing people complained about with Navi and Fi alike, and honestly it would be a huge potential risk with a human companion as they might be likely to say things of their own accord and get potentially very annoying and repetitive.
These both could be totally avoided and having such a partner
could be amazing -- as Bioshock Infinite itself indicates -- but it feels like it might be an odd fit for Zelda and, above all else, would raise an entirely new set of problems to overcome and things that need to be done right when frankly recent Zelda games are already struggling to correct a number of those. I wouldn't expect it any time soon at any rate. We'd likely have to wait for a Zelda game that's a lot more detailed in terms of world and character development first. Something that's a human, developing partner but whom isn't with you quite 24/7 as you adventure (like Linebeck) would be pretty easy to do though.
