Personally I think the threeway timeline is clever. Three timelines, three parts of the Triforce, three main characters(Link, Zelda, and Ganon)who have different affects on history.
I like to call the adult timeline the timeline of wisdom since it was Zelda's actions by sending OOT Link back to the past that removed the hero's bloodline which led there to be no hero to stop Ganondolf leading to the Gods sealing away Hyrule which sets up the games on the adult timeline.
I like to call the child timeline the timeline of courage since it was Link's actions after being sent back that changed history and sets up Twilight Princess.
I like to call the decline timeline the timeline of power since Ganondolf killing OOT Link sets up the events that lead into ALTTP.
Zelda's actions in the Adult timeline lead to the complete destruction of Hyrule... that don't seem so wise to me. In fact it seems more like she let her compassion outweigh her wisdom.
About the decline timeline and the "death" of OoT Link. Does it actually say anywhere that Link is killed? I seem to recall HH only stating that he's defeated, not necessarily killed.
Checking... Yeap.
HH P.92
"Of all possible outcomes, Link, the Hero of Time, faced
defeat at the hands of Ganondorf.
The thief obtained the three pieces of the Triforce, transformed into the Demon King,
Ganon, and continued to threaten the world in future eras.
The conflict surrounding the Triforce continued without end, the blood of the gods
weakened, and the kingdom of Hyrule shrank to a shadow of its former glory."
"THE HERO OF TIME'S
DEFEATThe Seven Sages Seal away the Demon King
Ganondorf the thief obtained the Triforce of Power and managed to
get his hands on Princess Zelda. The Hero of Time, Link, challenged
him in a battle that would determine Hyrule’s very existence, and
lost."
While it's possible Ganondorf kills Link, it's just as likely that he simply bests him and leaves him alive after taking the Triforce of Courage out of sheer arrogance which Ganondorf IS prone to.
Also I believe I found a plot hole (as defined as a contradiction in a plot) in HH.
HH P.92
"At last, Ganondorf found himself in the possession of the Triforce of
Wisdom that dwelt within Princess Zelda, and the Triforce of Courage
that dwelt in Link. His true power achieved, he transformed into the
Demon King. The Seven Sages of Hyrule, led by Princess Zelda,
sealed
Ganon and the Triforce in the Sacred Realm as a final resort."
HH P.93
"THE IMPRISONING WAR
For a brief time, it seemed as though peace
had returned to the kingdom.
However, there were many who knew of
the existence of the Triforce and the entrance
to the Sacred Realm because of the
events set in motion by Ganondorf. Their
lust aroused, they
rushed to gain access to
the holy land in their quest to obtain the
power of the gods.
Little did they realize that the Sacred
Realm had been transformed into the Dark
World by Ganondorf ’s evil heart. None
returned from their adventures. Instead,
only the power of darkness flowed forth."
"THE SACRED REALM IS SEALED BY THE SAGES
The king of Hyrule ordered the Seven Sages to seal the Sacred Realm.
The Knights of Hyrule guarded the sages as they offered up their
prayers, but demons descended upon them from within the Sacred
Realm, and a fierce battle unfolded in which the majority of the combatants
were killed.
The entrance to
the Sacred Realm was sealed once again, tight
enough that it should never have been reopened."
So...? When the hell did the Sacred Land get UNSEALED in the first place? It says plain as day that OoT Zelda and the rest of the sages sealed Ganon in the Sacred Realm. It doesn't say anything about that seal being weak. In fact if I take HH at face value, then OoT isn't the Imprisoning War at all.
If this is in fact the case then it kind of makes perfect sense that FSA was originally intended to be the Imprisoning War. I'm starting to think that the only reason FSA was placed after TP was because from a design point of view it's actually related to TP and Aonuma just didn't want it in the exiled Decline Era.