I've personally never played FSA, never beat FS, but I always thought that FS was just a way to make the sell of ALttP on GBA better. Make it more fun, if you will. After all, it was really only playable when you were linked with someone. That dosent make it a very accessible game. The main storyline games would have to be completely accessible, and follow the same general single player status as the others. Elsewise, there would be many people who would miss out on a good game just because they were unable to meet the requirements needed to play.
Also, I thought that FSA was a redone, bigger version of FS. I would consider FSA cannon, but not FS. Ganon's presence and story in the game makes it more believable. Althought I greatly disagreed with having to play it using a GBA. That's the reason I never bought it. It seemed more like a "Hey, try this new accessory out!" kinda deal, much like Link's Crossbow Training is for the Wii, advertising the Wii Zapper.
MC is cannon in my view, because there is no real reason for it not to be. It follows the same basic guidelines as all the other Zelda's and can be played by one person using the system itself and no extra add-ons. Majora's Mask and Phantom Hourglass are both spinoff games, cannon because they were sequels to cannon games. But none the less, they are spinoffs from the mainstream storyline. The Oracle Series were also spinoffs, but were cannon.
You can't really consider some canon and some not though, only FS maybe because of its limited accessibility. Cannon games are chosen by how they connect with a general timeline, and since the Zelda series has a confusing timeline, and one that has never been confirmed but guessed at a lot, no game can actually be considerred "cannon". But, since I believe in a timeline, I consider all of them cannon, other than FS. Oh yea, and those CD-i games.
