Seriously, I don't understand why people keep wanting Ganon as the main villain so much when if you think about it, he is basically an overused villain. I'm glad that Nintendo decided to take breaks from having Ganon as the main villain every once in a while. They've used him to death, hardly giving any of the other villains a chance, especially Dark/Shadow Link, considering he's been mostly a side villain or like in TP, a cameo villain who only appeared one time in that game in a single cutscene. This is why, I personally think the main villain for Zelda Wii U should be Shadow Link since according to TP, he is supposed to be the true leader of Dark Interlopers and the Incarnation that Demise was referring to. Yes, Demise eventually did reincarnate as Ganondorf, however another incarnation of Demise was born within Link, as to those who don't know or weren't paying that much attention, there is a scene in the beginning of SS in the Sealed Temple grounds area first visit part where Link is confronted with Demise in the form of the Imprisoned where Demise seemed to have placed a shadow curse on Link, which is what Demise was referring to when mentioned that Link bound by a curse and that because of that curse an incarnation of his hatred will follow Link's kind as well as maybe Zelda's kind, as he might of done the same to Zelda as well, considering there is such thing as Dark Zelda but it hasn't been confirmed official Zelda canon yet. Anyways in simple words, Demise is reborn as Ganon, the Incarnation of his hatred due to a shadow curse he placed into Link's mind as he was referring to at the end of SS becomes Shadow Link.
I also believe that because of shadow curse placed within Link's mind, this somehow caused the Silent Realm to become corrupted by darkness and overtime it became what is well known as the Twilight Realm from TP, as all that it was missing at that point was civilians, which is where the Interlopers come in. As the Dark Interlopers where slowly yet at the same time actually drastically rising up to power again, as Shadow Link is then fully awakened, leading various other Interlopers, they, the Dark Interlopers began invading the renewed and re-established Hyrule bringing major chaos upon the land, until they then sealed into the Twilight Realm where Shadow Link was born and came from. It is from there on, that the Dark Interlopers began to breed there and establish the Twili civilization. That is what I believe is what the "Era of Chaos" was all about.
Anyways, that is all I have to say for now. I'll speculate more on this another time.