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The way I understand it:
Ganondorf killed Link, meaning he got the Triforce of Courage, he probably bitchslapped Zelda or something like he did in WW to get her Triforce piece, thus giving him the complete set. As for why he did this, likely as a show of how unstoppable he is, on the level of typical James Bond villainy. He also didn't kill Link when he stood against him as a child in OoT and didn't kill him on their first meeting in the Forsaken Fortress/when he went to grab the Triforce. You might get away with saying he's genre savvy enough to know that he needed Link alive, initially, in both cases to lead him to the Triforce/pieces of the Triforce he needed, but even then, he really seems to have either some level of pragmatism or ego that makes him think leaving potential threats alive is a good idea. However, this is well within the realm of his personality.
1. As far as I'm aware, he only needed to incapacitate them, hence how he got the Triforce of Wisdom from an unconscious Zelda and just smacked Link around a bit to get the Triforce of Courage. Likely the only reason he left them alive was as "witnesses" to the rebirth of Hyrule. Again, his ego.
2. My guess is that he was mad with power. The Triforce reflected his inner-most self when he grabbed it, forming Ganon in that timeline (since that's the only one where he's gotten the whole Triforce), since he wasn't a balanced person making a wish.
3. In this moment, the sages simply ripped a hole leading to the Sacred Realm, put him in there, and sealed it back up. It wasn't a strong seal to incapacitate him (as it doesn't seem like he wreaked havoc in the Sacred Realm between the Adult Timeline and WW, only that he broke free). Trapping him in the Sacred Realm meant that he got free reign of it, which is why the Dark World existed in ALttP. He was sealed away out of desperation (something the backstory even references with the knights failing and the sages sealing him in the 11th hour of the war), which meant a shoddily made seal that didn't keep him from fucking up shit (basically, the same thing the sages did in TP).
4. Story and gameplay segregation. Hyrule is made up of more than 100 individuals, unless you really want to believe that there are that few people around and inbreeding is rampant. Also, as the series has always shown, Ganondorf and Ganon are among the most powerful beings in Hyrule, many orders of magnitude greater than pretty much anyone. However, not only do they have weaknesses (sometimes specific tools or weapons, other times, just their ego), but the games are built on an underlying message that Power isn't the only thing to consider when taking into consideration the strength of an individual. Link wins not because he's the most powerful, but because he outwits Ganon(dorf) and exploits his weaknesses.
5. Zelda needed to get the Light Arrows to Link somehow, because their best shot of being rid of Ganondorf was to defeat him. Plus, sealing him would likely require Zelda to be in close proximity to Ganondorf, the person hunting her down for having an artifact he needed. She thought she would be safe from him in the Temple of Time, but was wrong. Keep in mind, in addition to kidnapping Zelda, Ganondorf also had a barrier in his castle that prevented the Sages' influence from reaching him. Sages couldn't properly do shit to him as long as he remained in his castle, and by the time Link got rid of that barrier, Zelda was kidnapped and unable to help seal Ganondorf away.
6. Killing Ganondorf and getting the Triforce back is preferable to just sealing him away in his own little world to control until the point where he can unleash himself. Every time they've sealed him away somewhere, it's been a desperation move (OoT, ALttP's backstory, TP), and sealing in general doesn't work (ST, FS, FSA, and SS). They likely thought that having Link kill/defeat him would be the best option. What they didn't foresee, was the Triforce of Power giving Ganondorf invincibility and turning him into Ganon (after all, it was only a piece of the Triforce, not the whole thing). At that point, trying to separate him from the Triforce of Power wasn't an option, so they sealed him away in OoT because there bodaciously wasn't any other option.
I think the better question would be how Ganon didn't unseal himself with the Triforce in ALttP (which has been a hole since the game came out), or how Ganondorf in most other games is nigh-unkillable with just 1 piece of the Triforce, but the one game where he had the whole set was one of the few times he actually died for real (and then came back later).
_________________ -K-
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