Dude, ALttP downright states that the power through the sages/guardians weakened over time. Shrine maidens are NOT more powerful than sages, and we don't see sages in FSA. And using Occam's razor we know that the shrine maidens are related to the maidens.
First, I don't know what Occam's razor is. Second, I said absolutely nothing about the Shrine Maiden's or Sages powers nor did I compare them. So your entire response has little to do with anything I said. What I did say is that you have no proof that the Shrine Maidens are the same as the Maidens, or that they descended from the same groupe of people or anything. Shrine Maidens are maidens SPECIFICALLY of the Shrine of the Four Sword. That alone separates them from the other Maidens. By doing this, we only have proof that the ALttP Maidens are related to the Sages, whereas there is absolutlely no proof that the Shrine Maidens are related to the Sages.
Once again: How is LoZ Ganon ALttP Ganon when ALttP Ganon clearly died at the end of ALttP?
Original intent that has never been altered. Ganon didn't die at the end of ALttP, he was defeated. AST proves that Nintendo had ideas that Ganon was not fully dead. That whole plot may not mean much now, but an entire game was based around Ganon not being completely dead after ALttP and plus, since we know (or, most of us know) that Ganon in LoZ is the same, we know he didn't "die". Or maybe he did die and was brought back by unknown means, who knows? Who cares really? No one questions it. There doesn't have to be a "how" did he live or "why" didn't he die because we simply know he didn't. We know he's there in ALttP, we know he died the same way he did in LoZ, but there's a gap that no one knows what happened to him. All we know is he is alive for LoZ.
Why is it that in OoT the Gerudo look up to Ganondorf as a great leader while in FSA they look down upon him as a traitor?
Not all Gerudo looked up to Ganondorf. As a matter of fact, Nabooru did not like him at all. But, either way, Ganondorf had not done anything to the Gerudo people themselves during OoT. They had no reason to really hate him. In FSA, he broke into THEIR sacred pyramid and stole THEIR sacred artifact for his own greediness. Of course they would hate him.
Why is it that Ganondorf goes after the Trident in FSA instead of the Triforce?
Because the Triforce isn't an important factor of that game. Why is it that the Master Sword isn't there either? Because it isn't important. Plain and simple. The Four Sword Saga does not focus on either the Master Sword or the Triforce, whereas almost every other game does in some way. The FS Saga is like a break away from the rest, except for FSA which tries to tie-into the rest by including Ganon.
How can Ganondorf wish on the Triforce in ALttP when you can only wish upon the Triforce once?
Where is there any proof that you can only wish on it once? You can wish on it as many times as you find it and lay your hand on it as far as I'm concerned. What makes you think you only have one shot? And if you are suggesting that OoT is still the Seal War, how do you know he even wished on it in that game? And if he did, why is he even attempting to do it again in WW if he only had one shot at it? This just makes no sense really.
How can Ganon be the leader of a group of thieves for the Seal War when the Gerudo do not follow him in FSA?
Who's to say they are the same group of thieves? I mean sure, its likely that they are Gerudo people. But no matter what, he is their leader. Regardless of if they like or dislike him, the are more than likely going to follow him. But a number of things could have happened between FSA and the Seal War, such as an entire new generation of Gerudo being born under Ganondorf's control, or maybe he created his own new band of thieves since the Gerudo resented him. There could be many possibilities here that would work.
Why is it that Ganon is transformed by the Triforce in ALttP when by your standards he already should be transformed because of the Trident?
I never said the Triforce was the same as the Trident. I only said that when Ganondorf has had a source of power in the past, he had the ability to transform into a variation of Ganon. In OoT and TP, it was the Triforce of Power (also considering that in TP, he had Twilight power as well). That allowed him to transform into a variation of Ganon, but only for a limited time.
The way I see it, Ganondorf has always had the same beast within him at heart. That beast is, in part, a pig or something resembling a big pig monster. In OoT, TP, and FSA, Ganondorf acquired a source of power enabling him to transform into this beast, but it was different each time, I suppose depending on how the power affected him. In ALttP, his wish on the Triforce transformed everything in the SR into evil monsters because the land itself became infused with evil. Ganondorf himself was not saved from this transformation, which turned him into that which "reflected his heart". As I said before, his inner being is that of a pig monster. So his wish transformed him into a hybrid of this, but because it was the result of a wish and not a temporary source of power fueling the transformation, it left him in a permanent state of being that monster.