Some have said that Miyamoto's order is different because the games in Japan are different. Maybe their stories vary slightly. The title "A Link to the Past" doesn't mean anything at all - in Japan, the game was called "Triforce of the Gods."
But let's leave that behind us for a moment. Pretend for a moment that my current theory about OoT's ending is correct (if you don't know about it, go to my web site and read the article called "OoT's Ending, Revisited").
Link has been sent back in time and is young again. Ganondorf is foiled. Majora's Mask happens, and Link grows older and has a son, calling him Link after himself. The Zelda from OoT has a daughter, but a wizard puts her to sleep.
When the younger Link is ten years old, he leaves his father and goes off in search of adventure. Around this time, however, Ganondorf's wishes come true: stumbling into the Sacred Realm, he "steals the Triforce of Power from the people of Hyrule" and turns himself into Mandrag Ganon. The Triforce of Courage goes to the elder Link, while the Triforce of Wisdom goes to the younger Zelda because the older one is under a sleeping spell.
Ganon invades and conquers Hyrule, and the younger Zelda splits the Triforce of Wisdom and hides it. She sends Impa (who is old by now) to find someone to defeat Ganon, and Ganon imprisons Zelda. At this point, LoZ happens.
Meanwhile, the elder Link has the Triforce of Courage. He hides it in temples to keep in from Ganon, while the younger Link saves Zelda and defeats Ganon.
Years go by and AoL happens. Unfortunately, sometime later Ganon is revived by sacrificing Link and sprinkling his blood on Ganon's ashes, and Ganon steals the entire Triforce. The sages lock him in the Golden Land (the Imprisoning War), and four generations later ALttP happens. Like Miyamoto says, Link's Awakening could almost come anywhere in the series.
This theory could be made to work, but I personally think it's a little whacked up.