Garo
Boy Wonder
A previous Ganon? There are no multiple Ganons. If FSA is on the main canon, it'd be the OoT one, as he's described as a boy who grew up in the desert and was corrupted over time. That's a very accurate description of the Ganondorf that would have grown up in the Gerudo Desert. Plus we're told that by a Gerudo woman. She would have known the history of her people.
It isn't the OoT Ganon, though. The Ganon in FSA is described as being exiled by his tribe for exploring the desert pyramid, and thus becoming a desert nomad. Ganondorf in OoT, however, was not exiled and remained - if not King - a high ranking member, hence his presence in Hyrule Castle as a peace negotiator with the King. In addition to this Ganon, the Red maiden mentions hearing of a Ganondorf of the Gerudo before - the OoT Ganondorf. Two Ganons.
We haven't gotten Skyward Sword yet and you're placing a game before it? That's pretty dangerous. The only thing we can say is that it comes before OoT. And what I'm saying with references is that many games have made references to it to show where they are placed on the canon, such as WW, MM (mentioning Link waging battles across time and going on a personal mission), and TP. And those came after. If there's gonna be something before something as important as OoT, surely there'd be origins in it. Which is what they're doing in SS. I know I can't exacly prove this 100%, but there's really nothing to suggest that it goes there. Using negative evidence (almost always) isn't going to win arguments, especially something like you're suggesting. I'm not downing on your opinion, I'm just saying it's not a sound argument. So don't take me the wrong way.
Skyward Sword is the story of the creation of the Master Sword. Minish Cap has no reference to the Master Sword, and given the Master Sword's sanctity and importance to the Hyrule Royal Family later, it is unlikely that the Hyrule Royal Family would ignore the Master Sword in deference to the Picori Sword, which has none of the sanctity that the Master Sword does. Thus, it stands to reason that Skyward Sword takes place AFTER The Minish Cap, or at the very least in a Hyrule that has no Master Sword.