Here's how I see it langford.
Originally,
LoZ was the start of the series. Plain and simple. The basic good guy beats the bad guy and rescues the princess.
AoL is a clear sequel.
After that, I'd say the director's got to thinking "well hey...we pretty much just ended the series...now what? Let's make a prequel!" thus
aLttP.
Link's Awakening fits pretty well as a sequel to
aLttP
but then once again you're left with the "well now what?" attitude. thus, another prequel/sequel combo in
OoT and Majora's mask.
See what I mean? They keep finding 'dead ends' if you will, and then explaining things that were left up to question in the previous game.
After
OoT, there was the question of a possible timeline split...Wind Waker seemed to imply that there was one, but it could still pretty easily be a linear timeline.
I think it wasn't until after Wind Waker that they decided on a split for sure. That's why Twilight Princess was made. It pretty much confirms the split.
I'd say with each new game now, the timeline becomes clearer. Things are obviously much different then they thought at the start, but things are becoming clearer in my opinion. The split actually helped because it makes all the prequel/sequel nonsense more understandable. It's probably that
aLttP/
LA and
LoZ/
AoL aren't even on the same timeline now, so that makes up for the fact that both of those combos have a sort of 'end of the series' feel to them.