OoT Link had to have done something to stop him. For all we know, that's the big difference in a child timeline. Link's traveling back and forth through time and stuff did some things that helped with Hyrule and then his being in the "child time" after he completely saved the "adult time" helped in changing the events further. This could even explain why Link appears older in MM, rather than looking just as he did in the end of OoT. Really, I'm getting sick of wondering, I want someone from Nintendo to explain the connection between OoT and TP. It's obviously there, but I'm a bit confused as to what happened and what didn't happen if TP is in a child timeline.
I still maintain that FSA fits into the CT nicely if you place it immediately after OoT. Just assume Link went back in time to before he first met Zelda, and that last scene in OoT is them meeting all over again. Everyone agrees that if that were the case, Link would have to do something about Ganondorf:
Link: Uh, your highness, Ganondorf is trying to steal the Triforce.
King: Nonsense, Ganondorf was just here the other day telling me how nice my new shoes looked. Besides, noone can break into the Sacred Realm without removing the Master Sword, and evil people can't touch that. It's fool-proof.
Link: (well, I don't suppose telling him a tale of time-travelling will convince him)...well, he's been bothering the Zoras and the Gorons.
King: Really?
Link: Yeah. In fact, Darunia is pretty pissed that you're ignoring the whole crisis. 'Sworn Brother', all that jazz.
King: Oh, right. I'll look into that.
Link: You do that. I'll just get busy about lifting the curses he's placed all over the place.
(Later)
King: GANONDORF! You've been causing trouble all over the place!
Gerudos: GANONDORF! We thought you were cool! You loser!
Koume/Kotake: We still love ya, honey!
Ganondorf: Yeah, yeah, whatever. Get it over with.
King: BANISHED!!!
Ganondorf: Curses, foiled again! I'll be back!! In fact, I've heard about some fancy Dark Mirror off in the forest...(exit)
Zelda: Hey Link, there's this sword I want you to see.
Link: Seen the Master Sword already, babe. I wouldn't mess with it, though. Seven years in stasis isn't as trippy as it sounds.
Zelda: No, no, another sword. I've been sensing weakness in this seal that was placed on Vaati the Wind Mage centuries ago.
Link: Well, I HAVE been messing with the fabric of the space/time continuum, so yeah. No surprises there.
Vaati: I awake! I iz a big hit wit da laydeez! Come on Zelda, back to MY crib!
Zelda: Aaagh!
Vaati: WHAMMO!!
Link: I'll take care of this (removes sword, splits in four)
Green: To the Palace of Winds!
Blue: Chill, dude. It'll still be there in the morning.
Green: But the princess...
Red: Haven't you EVER played a Nintendo game? No matter how many times you save a princess, she immediately gets kidnapped again... so why bother rushing? So she can get kidnapped again sooner?
Purple: Word.
Green: Makes sense, I guess. Now that you mention it, Princess Peach IS kinda useless... I mean Zelda. Zelda, of course.
Purple: Word.
(One Purple Haze later)
Red: Whoa Blue, I don't swing that way.
Blue: It's not gay if we're the same person.
Green: All in favour of not letting Blue back in when we reunite after all this? Say Aye!
Red: Aye.
Blue: Nay!
Purple: Word.
Green: Motion carried.
Blue: Damn.
Green: Can we save Zelda NOW?
(skip to end of game)
Vaati: Aggh no, I'm melting... melting... what a world, what a world... No! Not inside the Four Sword again!
Links: QUEST COMPLETED! REUNITED! Not you, Blue.
Blue: Damn.
Ganondorf: Hmm, that Vaati fellow seems to have given them quite a bit of trouble. Now that I've stolen this Dark Mirror, I can make my glorious comeback! Go, Dark Link, kidnap the Shrine Maidens who are free to be the Sages without any contradiction since OoT's future never happened and I don't even know about it!
Link: Damn. Okay, Four Sword Time again! Blue, you can come too!
Blue: YAY!
Vaati: I awake! I iz a big hit wit da...
Links: shut up.
Vaati: Fine! Back to my crib!
Kaepora Gaebora: Hello, my name is...
Links: We've already met. You just don't remember because we went back in time...
Kaepora: I'll get me coat.
Links: good.
Scrubs: Yay Ganon!
Ganon: quiet! I'm stealing the Trident that I heard about in my youth!
Links: Zelda! We'll save you! Die, Vaati!
Vaati: I iz ded.
Zelda: Thanks, Links!
Ganon: Now that all the pieces are in place, I can crush you ALL!!
Links, Zelda: DENIED!!!
Ganon: Nooo, I'm inside a sword!
(later)
Link(reunited): Your highness, perhaps a more permanent solution to Ganon is called for?
King: Won't the Four Sword suffice?
Link: Vaati got out. TWICE.
King: Good point.
Link: Well, I'll let you deal with it. I've got a hankerin' to venture through spacetime again. I hear Termina is lovely this time of year.
King: I'll get right on that 'executing Ganon' thing. No procrastinating here. It definitely WON'T take centuries until some Sages finally get round to it.
Link: That would be best, alright.
King: Wow, I've just realised you've done a lot of cool stuff. You'll probably be remembered as a hero for centuries to come...
Link: ...
Link, King: NAAAAAAAH...