It's an interesting idea, but I think it's one of those things that's been done too much.
First, there is Fi, who is the spirit of the Master Sword. Link's companion is his sword. Awesome. Now that it's been done, there needs to be a new kind of companion, or a new game should go old school and have Link on his own.
I've recently gone through watching an anime called Soul Eater. You've probably heard of it, it's fairly popular. People and weapons-who-are-companions is pretty much the entire premise of the series. (That and collecting souls for the Grim Reaper and fighting an evil god of madness). In that world, magic and witches exist and 800 years ago, some witches experimented with creating living weapons, which means, in the present day, present time, magical weapons are a race of people. You can be born a weapon - having a human form and an alternate weapon-form and people who are capable of using these weapons wield them in a partnership. The main characters are a teen girl and her scythe-who-is-a-teen-boy. Since Soul Eater pretty much takes the whole companion/weapon convention up to eleven, I don't see how Zelda could do anymore with partners like Fi without looking like the series is copying or in some way, unoriginal.
(Fi operated differently than the weapon-people in SE, but, still... emphatic weapons are a concept that's been done to death in fantasy fiction).
