Demonic Spiders: Any time Shadow Link manifests in the air. He's invincible like this and will repeatedly drop Giant Bombs on you; all you can do is avoid them until you escape the area.
Fanon: Shadow Link spawned a ton of it; chances are if it's not of Ocarina of Time's Dark Link, it'll be of this one. The manga definitely helped this along.
Fanon Discontinuity: Many fans like to discount FSA due to the continuity issues, and depressing implications about fate being unavoidable especially for the Gerudo and Ganondorf particularly for fans who dislike how Ganondorf is the product of Demise's curse. It helps that Miyamoto wrote the plot without continuity in mind.
It's the Same, Now It Sucks!: Some argue that they recycled too many graphic assets from previous games, even if they were enhanced. Plus, some argue that it plays too similar to the GBA version (despite that FSA blows it out of the water in every possible sense), if not to A Link to the Past itself, since it uses many items from that game.
Rewatch Bonus: After the release of Hyrule Historia, going through the story again becomes much clearer in that the Ganon of this game originates from a new Ganondorf, not from the same one originating in Ocarina of Time.
If a GBA is disconnected, the game freezes for a while before returning to the title screen if the controller is not reconnected. This only allows enough time for the event of the cable accidentally being unplugged. If the batteries in your GBA died you better hope you saved recently. Worse yet, the design of the GBA SP and the GBA-GCN cable combined means you can't have an SP plugged in with an AC adapter at the same time you have it connected to the GCN.)
The fact that you needed to buy a GBA and a connector cable to begin with is bad enough. When the game was released, that would be almost 200 bucks down the drain if you didn't already have a GBA, and nowadays it's maybe $50-80 on the used games market, but almost impossible to find.
They Changed It, Now It Sucks!: It's a multiplayerZelda game, so that should say everything. Yes, there is a compelling single player mode... in which you play four Links at the same time and it has no overworld in the classic sense of the franchise.
What an Idiot!: Given Ganondorf's bad reputation at this point, the Gerudo naming the new King/Guardian was asking for trouble.
Foe Yay: Shadow and Vio, especially since Shadow states he really did consider him a friend and actually seems hurt by The Reveal that Vio has lying to him about joining him. There's also at least a hint of it with Shadow and Zelda.
Fridge Brilliance: Each of the three Links created by the Four Sword matches one of the the three virtues of the Triforce. Blue is a strong, aggressive fighter (Power), Vio is analytical and calculating (Wisdom), and Red is willing to fight alongside the other Links despite his inadequacies and relative weakness (Courage).
Take That, Scrappy!: Unintentionally, this manga gives plenty of this the American haters of Tingle when Vio beats him with a sledge hammer, and later when he complains about being left out of the finale of the manga, it's revealed the reader didn't see him because he was crushed by a giant force gem.
Alternative Title(s):The Legend Of Zelda Four Swords 2004