I remember reading those statements by Aunoma, in which he said (I'm going to paraphrase this, as I'm too lazy to find the actual interviews) Ganon wouldn't be appearing in the game, but SS would somewhat explain how he came to be the nemesis in OoT that we all loved to hate. I also remember thinking to myself, "Self, are you there? Is there a word for foreshadowing in Japanese? 'Cause it sounds an awful lot like that's what he's trying to say, and maybe we're just loosing a little something in translation? Keep up the good work, Self, you dashingly handsome devil you."
So, going with that interpretation of Aunoma's words: I gather that Ganondorf will not appear in the game (as I presume he hasn't even been born yet, though I have no idea how long people, let alone Gerudo men, live in Zelda lore); but events will transpire within the plot that foreshadow his rise, and or corruption that have clearly already happened by the beginning of OoT. That said, it begs the question: how do you foreshadow a man's rise, and or corruption, without him being within the plot itself? I think there's a few different ways of doing that, with varying levels of effectiveness and dramatic importance. I'll list a few methods that have popped into my head, but with the disclaimer that while I am trying to think logically (in an algebraic manner) it really is utter speculation. Now then:
-Link may meet one of Ganondorf's parents, who will perhaps mumble something about naming their unborn child "Ganondorf". (While that would classify as foreshadowing, this example seems a little too unimportant an event to me, or to justify Aunoma even mentioning it.)
-Link may encounter a small boy, or even infant named Ganondorf, and this child may at some point be spirited away by the witches that comprise Twinrova, of which I've forgotten the names. (This is foreshadowing as well, and also seems a more significant event than the prior example; but it doesn't really sit well with me, as it doesn't quite explain why he's so driven to take over the world.)
-Perhaps Link will defeat Ghirahim's master, at least in form, and its remaining malevolent spirit finds its way to the infant Ganondorf or one of his ancestors, and then fuses with that person. Heck, maybe Ghirahim's resurrection plot even involves the finding of a new body for his master to inhabit (in something akin to possession), and that body is to be an unborn Ganondorf, or one of his ancestors. Or perhaps a blending of those two related ideas. (That's definately foreshadowing, explains Ganondorf's desire to rule the world, and a sufficiently significant event to justify Aunoma's comments in interview; but also keep in mind, I know while that theory is walking about in a nicely tailored logic suit, it's still wearing speculation underwear.)
It should be obvious that the last point seems the most likely to me (and the most nerdgasimly satisfying), though I should overtly explain the variables and subsequent math that's lead me to that inclination (remember to show your work kids):
1. The forging of the Master Sword. At some point within the game it will happen, and I imagine in true fantasy form, it will be made out of necessity to specifically defeat Ghirahim's master.
2. Aunoma's comments about the explanation (or foreshadowing) within SS of Ganon's appearance in Oot
3. The Master Sword seems to be Link's weapon against Ganon in most of the games they both inhabit, much like Vaati and the Four Sword (I don't really count Four Sword Adventures, or whatever the game was called that featured Vaati, the Four Sword and Ganon. It felt more like a Zelda Party game than an actual LoZ story, and seemed a bit confused with its placement or identity).
4. Throughout the games (Even way back during my first playthrough of ALttP), the impression grew within me that the Master Sword was perhaps intended by its makers as a bane, or counter, to either Ganon or the misuse of the triforce. There was nothing said directly to that effect, and so it really was just a feeling; but by design or not, that feeling came quite easily to myself and many others; so I wonder how aware Nintendo was of that 'impression' in the making of SS.
5. The main baddie in the SS intro does bare at least some resemblance to Ganon's beast form (though to be fair, it also resembles something I've scraped off my shoe as well).
Ergo, my math is as such: Presuming that the Master Sword will be forged to specifically defeat said baddie (as it no doubt will), my third foreshadowing example would fit nicely in as an explanation to why Ganondorf seems so keen on repeatedly getting the happy end of the Master Sword in his squishy bits, without him appearing in person within SS. Not because it was forged for him, as myself and others had felt, but rather the force within him that is Girahim's master, be its name Ganon, or King of Darkness, or... Tim.
You have to admit, that theory does seem to work. However, if I am completely off base (which is quite possible), I do hope the reality is superior to that theory. It'd be a shame for Ganondorf's "OoT explanation" to fall short of something that effortlessly popped into some of our minds.
As final note: I don't think Ganon is a tired character, or plot point. Quite the opposite in fact; he's an integral part of the Zelda Trio when the Triforce is a feature. If he feels tired as a character, I'd say it's rather that individual game plot that's failed, not the character (I'm looking at you Four Sword Adventures). However, even in his more criticized recent role, Ganon felt epic to me in TP. From the moment I noticed Link's Triforce of Courage mark on his hand (an example of foreshadowing, quite early in the game), Zant felt out of place as the main baddie. That Twili felt intimidating as a powerful sorcerer; but he didn't feel like he belonged in that role, as he wasn't crushing-the-world-under-his-boot powerful like Ganon was.
My speculation underwear has triforces on it.
