This thread is in need of an update. Since I can't edit my original post, I'll just add the new stuff here.
Sky Loft: Home of the Oocca
While playing through TP again, I came across the image of Ooccoo, or a similar-looking Oocca, in the cellar of a Kakariko house. From what I remember from playing it at release, this cellar plays an important role in the Oocca storyline. (no spoilers please, unless it is vital to this discussion. I have very bad memory and haven't gotten to that part yet.) What worried me is the fact that this supposedly ancent Oocca is depicted in the same bird form as seen in the present, meaning Link in SS wouldn't fit that description. While retconning may be bad storytelling, I'd rather Nintendo hand-wave one simple drawing than completely contradict the story they introduced to us in the last console game. Why tell us that there's a race closer to the gods that live in the sky, only to turn around and say that the Hylians themselves lived in the sky the first chance they get?
Timeline Placement: The Beginning
This has since been confirmed, and SS-MC-OoT denied. It is now SS-OoT-MC, which fits my theory perfectly.
The Skyward Sword: the Driving Force for the Heroic Return
Aonuma stated that while the mysterious figure is feminine, it is not necessarily 'female'. I'd say this means it's not the Fiary Queen, a Great Fairy, or a Sage. It's probably some new entity that hasn't been introduced before. Otherwise, the rest of my theory here stands.
The Evil Forces of the Land: Another story from Twilight Princess
Playing through TP again has brought up some connections between the interlopers and the Shiekah in my mind. I hope they explore this (whether bolsering it or shattering it).
Some more things to note about my theory:
-SS Link is not the Hero's Shade. I think he is (nearly) specifically stated to be the HoT in-game (TP).
-SS Link is not the Hero of Men. The HoM backstory is inconsistent with what we know so far of SS.
-SS will not involve the Sleeping Zelda Story. This can only happen at a time when the Triforce is split and in the hands of the King, and it will obviously still be in the SR in this game.
In response to other replies:
Thank you all for your interest and support, thank you jones for the lolz, and as I said, the mysterious figure is probably not the Fairy Queen, or Midna for that matter.