The "timeline" wasn't particularly a serious part of the series until they made it confusing, ironically.

Zelda II was always the sequel to Zelda I
LttP was suppose to be the "Golden Age" mentioned in the manual of Zelda II
OoT was suppose to be the "Sealing War" mentioned in LttP's opening crawl
Majora's Mask was always the sequel to OoT.
The Game Boy games were always nebulous.

Wind Waker/Twilight Princess is where everything falls apart as they both take place 100 years after OoT. Even funnier is that Wind Waker is the one that actually brings up the idea that Link is the same person being reincarnated across time... only for it to be explicitly stated that WW Link is just some kid.