If you are trying to prove your theory about the Zelda storyline, it is important to lay down some ground rules. Depending on what aspect of the canon you are using for proof, some arguments are stronger than others.

The first thing to remember is that older games weren't as carefully made, and they left out a lot of storyline details. Newer games pay more attention to details and consistency. It is therefore easier to prove a theory about the newer games, simply because the newer games give more specific, unambiguous facts.

In any good proof, it is important to use quotes. I consider quotes from the games and manuals to be of equal weight, so one can quote from either with equal confidence. Arguments based on artwork are generally weak, and should be backed up by textual evidence when possible. Arguments based on gameplay are the weakest of all, and should not be the main basis of any theory. Every theory based on gameplay that I have ever seen has been mired with inconsistencies and ambiguities. Gameplay evidence can back up a theory, but usually doesn't prove anything conclusively.

My final word of advice is: use common sense. Maybe I'm a bit conservative when it comes to the Zelda storyline, but when I see grandiose theories based on scanty evidence, all I can do is shake my head sadly. I'm not the expert on relative canonicity. Much of this is up in the air. But the best we can do is try to rely on clear thinking and common sense, and not get sidetracked by features of Zelda that are there only because Hyrule's history happens to be presented in games.