A Male born every 100 years, this is the Gerudo way. Ganondorf is the latest male and he never really lost to link. He lost to himself. This dose sound odd indeed, but it is true. When ever he gets beaten to a pulp, it is because of his own faults, no Link's superb sword skills and the cleaver thinking of the player behind the controller. Greed, power and envoy has beaten Ganondorf every time when he encounters Link. But, the greatest weakness that Ganondorf has is his incompetence. Let me explain. Zelda 64, the beginning of the Saga was one of the most embarrassing defeats for Ganondorf indeed. He simply under-estimated Link. He had all the facts, he had the Triforce, Zelda and the home court advantage, and he still lost. His use of receptive attacks was his downfall. The same lightening bolt fired at Link was his secret message for asking "Link, please hammer me into the ground, I wanna come back next time!" Also, when he turned into Ganon, his massive swords took up most of his brain power with sheer anger. He was embarrassed once, but not again. Or at least he thought. Once again, he got repetitive. The sword movements and leaving his tail vulnerable were predictable at best. He should have learned when he got beat the first time in the tower, being repetitive leads to getting your @ss beat. Ganondorf should have realized that he had a piece of the Triforce, and knew how to use it. He thought that it would be an easy victory and got sloppy.

In Link to the Past, his repetitiveness got him into more trouble than before. You think he should have learned when he got beat and imprisoned the first time. He certainly had enough time to think about it. Now, this is where his ignorance comes in. Instead of just setting up shop in his tower, he should have removed that corrupted fairy in the tower first. Without her, the silver arrows and upgraded sword wouldn't be possible to obtain, and Link couldn't defeat him even if he was 10 times better than Ganondorf. Second, new moves aren't enough. If you have a cancer, you have to cut it out and Link was that cancer. He shouldn't have used those tired moves as a last resort, he should have finished him when he was fighting those dungeon bosses. No Link, no hero, no loss. Third, instead of using crystals to keep those maidens in check and given them to his minions, who weren't that capable of taking care of them, he should have kept them with him, or even better destroyed them and find another way to keep his agenda in check. Without those silly crystals, Link wouldn't have been able to enter his tower on Death Mountain. Therefore, he would have been able to keep him where he wanted and set him up for the fall. All of those factors could have ended the battle a long time ago, but he had to get over confident and decide that he could beat him with one finger. Fool.

Now, here's where it can get a bit confusing. In Z64, when entering the Forest Temple, you have to beat up the Poe sisters and then enter the gallery to fight Ganondorf on a horse, not Phantom Ganon, but Ganondorf. You see, when I said before that he had a lot of time to think about beating Link and revise his plan, he did. Since the locked up Ganondorf had already knew the out come of his demise and being locked up inside a void in time, he could be able to plan better for the past, not the future. Since he can't send him self personally back to the past without his captors knowing that he had escaped, he sent a PHANTOM hence the name Phantom Ganon. You can sort of considered this his last ditch effort to get a victory. Unbeknownst to Ganondorf in the past before the defeat, Link had enter the new future to stop him from ruling the world. This catches Ganondorf off guard, luckily he comes to the rescue, Ganondorf's phantom. After the last ditch effort going awry, Ganondorf the ruler of the world, finds where Link is and realizes that there was a fight, trying not to look stupid and unprepared to his enemy, he makes up that whole line of garbage about he sending the phantom and indirectly sends his own self into the void, condemning himself to his own prison. Since neither of the Ganondorfs' know this, they blame Link and the sages and vow to get their revenge, but their revenge belongs to themselves.