They had no timeline in mind when designing the games, so this is just the games shoehorned into a timeline after the fact, there's going to be inconsistencies. They should just finally settle it and explain how there's no Zelda canon, besides the games that have direct sequels.
References to past games does not mean there's a canon timeline, the Link in most of the games is a different person altogether. You could also say each game is a different "legend" about the same event. (namely, the defeat of Ganon)
Like I said, it was established after the fact. Most sequels in gaming are an afterthought. Also, you can't just say each game is a different legend of the same events because many of the games refer to past games' events in one way or another. These games are obviously taking place in the same universe, mostly in the land of Hyrule. Hyrule is always a very different place, with those differences playing directly into key events in the Zelda timeline (such as the Imprisoning War, the Great Flood, legends of the Hero of Time or Hero of Men, etc.).
Skyward Sword makes this very clear (big spoilers):
Spoiler The game is set before the land below is even known as Hyrule and before Zelda's family became royalty of that land. The recurring Master Sword is created in this game and the Demon King Demise makes it clear that he (Ganon, who seeks the Triforce), the chosen hero (Link's incarnations) and the descendant of the Goddess Hylia (Zelda's incarnations) are locked in a never-ending struggle.
I don't think anyone that's familiar with Zelda's lore could say that the vast majority of the games aren't part of some sort of timeline.