I have read some interesting time line theories regarding Zelda. Here is how the truth abou the Zelda time line is.
The various Zelda games do have an order where they take place in regards to a Hyrulean history.
OoT
MM
WW, PH
TP
....
LttP
Zelda
AoL
blah blah blah
However there is an important fact to this. There is little in regards to hard historical connection that their is a solid order of game time line.
Many large scale events occur in the Zelda games, mostly in regards to OoT, LttP, Zelda and AoL. Improsining War(wich really wasn't a war), descendents of the oracles(lttp), Ganon being free(Zelda NES) and the end of the series(AoL).
The dual timeline while probably the best of the theories is in fact just a shoehorn method to bind the game series. Miyamoto has admited that each Zelda really is it's own universe of Zelda. Miyamoto and now Anomura will scrap continuity in favor of the current game story and play. Though Anamura does care a little more on doing some binding(picture of the fisherman from OoT in TP), Town names in AoL matching Oracles from OoT.
It's taken me 5 years to admit that their is no factual timeline, but that's the truth of it. Is it fun yes. For fun I have done a Zelda PnP rpg and shoe horned a timeline, but I do accept that their isn't a real one.