This is a rather unusual timeline theory but i think it does a lot to explain connections between the games.
/ WW-
PH-
ST- AolBS-
Loz-
AoL- OoX\
MC-
OOT ---------------------------------------------- ------LA
\MM-
FS-
FSA-
TP- (Zwii?)-
ALttp-OoY /
The Minish Cap comes first, obviously arguable, but plausible,
OOT- Duh
AT:
WW/
PH follow
Oot
ST- 100 yrs after
PH - obviously not set in stone the game could change the order
AOLBS- any other time in which the triforce is split, up creates serious flaws
Loz - the master sword is gone after WW, and its potential dislodging from ganondorf's head, (will get into later) leads to the appearance of Ganon in the
Loz/
AoL
OoA-
OoS- now I'm assuming that the MS in OOX is canon because while its not necesary to beat ganon, doing it with out it is a royal pain, additionally, there are 2 ways to get the master Sword, from a Zora, who found it in the Water (WW ending much?) and from the Forest (
TP/
Alttp?)
CT:
MM: duh
FS/
FSA- this explains how a "new ganon" was born, and solves the potential problem with mirrors if the dark mirror and Mirror of Twilight are the same (still have no opinion on that one) Also, it helps solidify the single ganon theory, which i generally support. Its the same gannon from
Oot, he just doesn't get the Triforce, After being sealed in the
FS they decide to execute him.
TP- this is where it gets a bit fuzzier
ganon arguably dies at the end,
I believe that the Triforce stayed in the Sacred realm and the powers granted were much like the
AoL crest on Links hand,
ZWii?- no real proof of this, just a feeling since, the appearence of ganon in
Alttp is still unexplained
Alttp- this is the weakest piont of the timeline
I don't really have an explaination for how ganon got into the DW, the triforce (theoretically anyway) is still there though)
OoS-
OoA- this unifies the timeline, the triforce is present in the
Alttp ending, and in addition to the MS coming from the forest in the opening of the two games, one starts on water, while they other starts on land, which leads one to believe that they are on seperate timelines.
LA: this is the last game (so far) it solves the question of where it goes because it follows
AoL,
ALttP, OOX and OOY solving much of the controversy here
This is my Timeline theory IK its not perfect,
Alternatively to resolve the
Alttp issue, i would put it as
/ WW-
PH-
ST- AolBS-
Loz-
AoL- OoX \
-
OOT ---------------------------------------------- LA- MC-
FS-
FSA-
ALttp
\ MM--
TP- (Zwii?)-- OoY/
the MS is still in the forest in TPand this solves many of the geography issues, which i was previously ignoring, Under this theory, OOZ created the Trident, allowing it to become a vessel of Ganon's spirit, leading to
FSA/
Alttp