In essence: what makes your timeline unique?
At the time I began mine, most timelines tended to slant towards the
ALttP/
LA-
LoZ/
AoL order and put the 2D games on the Child Timeline. Mine was unique in that it followed the Miyamoto Order, in fact supporting it using scenarios from
TWW and
PH's links to
AoL and the Four Sword games.
Things that I've pioneered:
1) The Miyamoto Order in the modern timeline. I was among the first modern theorists to review
LoZ/
AoL in the context of
TWW's flood. One of the first hints to a chronology was the common reference point of the "time when Hyrule was one kingdom," referenced as history in
LoZ/
AoL, set down as the time period of
ALttP's backstory, and explicitly cast as the setting of
OoT.
TWW would mark the ending of that period, the decline of the Hylian race and language as referenced in
ALttP, and a period in which a new king would be sought for as described in
AoL. Since
TWW also places a high emphasis on the naming of Princess Zelda, it also seems to share connections to the naming tradition of
AoL. This combined with the search for new lands in an ocean-based world plus
AoL's unique inclusion of two additional islands in Hyrule's jurisdiction seemed to cement the
TWW-
LoZ/
AoL order for me, especially once I noticed that a portion of
PH's sea corresponds roughly to
AoL's map.*
*Goron Island matches Death Mountain; the Isles of Ruins and of the Dead closely match the large islands; Maze Island is in about the same place relevant to said islands.
2) The Naming Tradition pre-Flood. I associated the naming of Zelda in
TWW with the naming tradition laid down when the "first generation" Zelda was put to sleep, setting the establishment of this tradition in the aftermath of
OoT, when the Triforce first passed into the hands of the royal family. This looser interpretation of the Sleeping Zelda story led to a loose interpretation of the Hiding of the Triforce of Courage as well, allowing for it to happen as a result of Daphnes's wish at the end of
TWW- he leaves behind the Triforce for a time when a new king would come and establish the kingdom he wishes for for his descendants.
3) The sealing of the Four Sword in the Sacred Realm. The maidens cast a seal on the Four Sword in the ending scene of
FSA that bears a strong resemblance to the depiction of the seal on Ganon first shown in official art for
ALttP and later in a stained glass window in
TWW. I interpret this to mean that the Four Sword was itself sealed in the Sacred Realm by the maidens, allowing for the Palace of the Four Sword to be canon and setting up
FSA as
ALttP's direct prequel.
4) The Cobble as simultaneously descendants of the Hylians and the pyramid-building ancestors of the Zuna. The Cobble have the Hylians' long ears but also have the pyramid-building legacy referenced in
FSA for the Zunas' ancestors. While this theory is really irrelevant, it does seem to serve as subtle background evidence for the 2D games' placement in the Adult Timeline.
5)
OoT as
still being the Imprisoning War, despite a direct connection to
ALttP being impossible. Instead of being a direct story as to how the villain got to where he is (as it is told in the SNES manual), the Imprisoning War seems to have been reduced to a backdrop explaining the sages' seal (as it is told in the GBA manual), which the villain is now trying to break.
FSA seems to have offered a new backstory for
ALttP's Ganon.
6) The Great Deku Tree uniting the islands and expanding them to create the Hyrule seen in the 2D games. At first this idea was met with much criticism, but the Deku Tree's appearance in a post-Flood world that features some locales from Hyule in TFPRR gives me hope that this is something at least loosely incorporated by the developers.