Hmm. You may be on to something. Maybe FSA was Ganon's actual backstory. Maybe OOT's Ganon is a clone like ciela and Oshus were clones in PH. FSA does fit nicely before OOT now that I think about it. Ganon could have been trying to break the FSA seal in OOT and partially succeded. He then lasts a few centuries (possibly millienia) and dies in TWW. It also would explain why Vaati wasn't known of in TP. I sure hope that Zelda Wii and ST help with this.What connections? Surely you aren't talking about geography and paltry cameos? Because they aren't solid connections. A more correct answear would be that there was solid connections, but they where removed after a certain upending the tea table, and because of that the games aren't related by story anymore. There's actually no reason for them to be a pair, and the developer have never ever even mentioned ALTTP in the same sentence as FSA. Yet they have, given us a straight foward placement for FSA. It is not stupid to think that the developer are right. It's these all-knowledgeable fans who are stupid for dismissing Aonuma own word in order to embrace something that might not mean anything at all!
Clones!? Don't be ridiculus. There's only one Ganondorf. Just like there's only one Link, Zelda, Tingle, and Malon. There's also only one Fado too and he/she/it always stays the same gender/race/age.