Multiple timelines could fix a lot. But there are no quotes about it..... well there is rumour. Remember my Gamepro quote about WW? The one that appeared to a be a reprinting of Nintendo power and EGM? There is a RUMOUR about an UNCUT version of that interview at the windwaker summit in 02. The translation of the alledged interview is as follows. but is is very specious and NEVER made it to print (which brings to mind the question who leaked it and why didn't they print it? or is it legit at all or just some kids imagination and lies as I have no LEGIT source for this other then rumours of an "uncut" interview) In my experience uncut interviews are usually crap. I heard an uncut interview with the president of Rare saying that Rare was making Perfect Dark for DS but it turned out they didn't even GET dev kits for DS for some time after that. So take a gigantic grain of salt with this.
Miyamoto: Well, wait, which point does the hundred years start from?
Aonuma: From the end.
Miyamoto: No, I mean, as a child or as a...
Aonuma: Oh, right, let me elaborate on that. Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place hundreds of years after the adult Link defeats Ganon at the end of Ocarina.
Miyamoto: This is pretty confusing for us, too. (laughs) So be careful.
(this makes sense to me cause there is stainglass of the sages of OoT in WW, if the timeline takes up from the kid line those new sages were never instituted. but that doesn't mean this interview ever occured)
HOWEVER! I do have an interview from Nintendo.com
Games : Developer : Legend of Zelda, The: The Wind Waker in which Eiji seems to advocated a split timeline. I will say the 100years is a mistranslations judging from other problems with translation and clarifications i think he means 100s of years.
HOWEVER! if this is indeed what is intended then the interview with Miyamoto clears up a LOT.
MC
FS advance
FS Adventure
Imprioning War
OoT
at the OoT point the game splits.
adult Link goes on to
Soul Calibur 2 (he has Ocarina of time unlike child Link)
WW (Ganon escapes Sacred realm
PH (link appears to go on another strengthening quest
Oracles (New Link fights revived Ganon)
Child Link goes on to
MM (Triforce of wisdom goes back to Hyrule when Link enters Termina)
TP (Ganon escapes with Zant, is defeated, Ganon dies, Royal family keeps power and wisdom)
LoZ (someones blood brings Ganon back, he swipes power)
LoZ2AoL (TP Link's triforce of courage is buried deep in the last dungeon and the triforce is completed)
LA (link goes sailing to strengthen himself)
aincent tablets.
LTTP (Agahnim uses blood to bring him back, Link beats him, makes his wish, master sword sleeps forever, sacrd realm FINALLY purified)