Really Nintendo clould not have had the entire timeline laid out before they started making Zelda games. In fact when OoT came out the split timeline didn't even exist.
Of course not. They choose a placement relative to the existing games each time they make a new one, but I don't think they've always thought of it as a "timeline," not until there were a number of games. And I'd like to point out that the split did exist when
Ocarina of Time first came out, but of course there wasn't a whole alternate timeline until
The Wind Waker. But now I'm rambling. Let me answer the thread.
Obviously,
The Legend of Zelda was technically originally the first in the timeline, until they released
A Link to the Past which was intended as a prequel and then
Ocarina of Time which was a prequel to that. After that, until
Skyward Sword, each game almost certainly comes later (I'll explain some of that below). Now
Skyward Sword has obviously been stated to be a prequel to
Ocarina of Time. That's what was specifically stated - it's worth noting that they did not state that it's first in the timeline. It obviously is at this point as they have made no games that can come before it. I think they didn't say it was first so that they could make a prequel to
Skyward Sword at some point in the future if they so desire (no plans there, just leaving the option open for themselves).
But now for the thing with games coming after
Ocarina of Time. It's fairly obvious with most games released since it, but the one game that seems to have a quarrel is
The Minish Cap. People seem to say "maybe it comes before
Ocarina of Time" because they fail to realize why it must come later. In
The Minish Cap, it is well established that the royal family has been well established for generations. During the game, you visit the tomb of King Gustaf, who states that he ruled "countless ages ago," whereas in
Ocarina of Time it's indicated that the kingdom of Hyrule has only existed as a kingdom for about a decade, and the war uniting Hyrule has much to do with Link's birth and how he ended up in Kokiri Forest. Then, obviously,
Skyward Sword takes place prior to Hyrule's existence as a proper kingdom.
