Where do the names of characters like Morshu, Fari and Gwonam come from? I would assume that they're from the enclosed instruction book, but I haven't found proof that a manual or guide even exists.
As it is written : Koridai has fallen to Ganon and his evil friends! The gentle islanders are being transformed into blood-thirsty warriors. As you speed towards Koridai on Gwonam's magic carpet, you have only one thought: find Ganon and defeat him. Restore the peace and liberate the citizens of Koridai!
The Hyrule Alphabet has never been published for research. Morshu, Fari, and Gwonam could easily be common names in Hylian.
Anyway, the names Gwonam and Morshu appear in the manual here 
Fari, at least, if memory serves, was created because of Youtube Poop, where the guy wanted to give the nameless character a name and therefore used some line by Gwonam backwards that sounded like "Fari", which then people that never played the games started to accept as his official name. At least I think that's how it went.
How come "only Link can defeat Ganon", but Zelda is the star of the other two?
Gwonam can't read. Alternatively, his secondary language is English Hylian, and he has studied it so much that he forgot whatever the Hell language "Squadala" is in, which is also the language the supposed prophecy is written in. The only word of his original language he remembers is "Squadala."
Maybe the prophecy was "only Link can defeat Ganon in Koridai."
Or maybe it's actually "only Link can kill Ganon" and he mistranslated it.
Wait. If there wasn't enough time for Link to bring anything but his sword, why was there enough time for Gwonam to let Link wander around until he found his house before he gave Link what he needed to reach Ganon's lair?
He likely had no items to imprison Ganon anyway, and the sword sucked at first. I doubt this one Link had Silver Arrows.
Why did CD-I Zelda say that CD-I Link "did not" just save her from Gannon, despite irrefutable evidence that he did, in fact, save her from Gannon?
He kidnapped her IN THE DARKEST NIGHTMARE HOUR, while she was still asleep. She didn't wake up until after Link had already killed Ganon.
Ganon is depicted with green skin instead of purple like in all games before this. After that this he was depicted with green. Does that mean it isn't completely discontinued by Nintendo, and actually inspired this aspect?
Here's an official poster released by Nintendo featuring "each version of Link from the original The Legend of Zelda game for the Nintendo Entertainment System in 1987 through The Legend of Zelda: Phantom Hourglass for the Nintendo DS in system in 2007." See the Cd-i games anywhere?
King Harkinian took the Triforce of Courage to protect himself, leaving Link defenceless against Wizzrobe's spell.
Can someone explain to me what was with the weird gestures the characters did when they talked? For instance, in the beginning cutscenes of Wand of Gamelon, Zelda says "A whole month gone, and still no word." As she says this, she makes a circle motion with her right fist in front of her eye and points to the top of the screen with her left. Um...WTF is all I can say.
Most people believe that she's crying, and she's rubbing her eye(s?). Of course, considering the animation quality, Your Mileage May Vary.
Why is it that the "normal" people in these games (like the pedophile shopkeeper in Wand of Gamelon and the crazy cloak lady) are the ones that are really creepy, while the villains look absolutely ridiculous?
TO put it into perspective: these guys fail at everything. Anything they do gets turned on its head. If they wanted to make a normal, average person, we'd get a wrinkled, hideous humanoid. When they try to make a villian, we get this
Ushrom and the cloak-lady are supposed to be crazy (look at those eyes!), though there are sane NPCs, like the librarian in Faces of Evil. Speaking about Ganon - this is the first Ganon, who is not a blue pig! In fact, he looks like Ganondorf's first form from Ocarina of Time: darkgreen skin, red-green=brown cape, sorcerer abilities. The developers were freaking prophets!
What does "squadalah" mean?
Letsa go! Or else MAH CAKES WILL BURN!
It's a magic spell to fly.
Why couldn't Morshu give Link credit?
Jokes aside, Morshu, as well as most shopkeepers, care only about their wallet and not the good of the world. Of course he couldn't just loan bombs to every passing elf.
Or lamp oil, or rope...
Why didn't the Triforce of Courage protect the King?
I assume that Gwonam was either speaking metaphorically and saying that Glutko the monster was guarding the Shrine of Koridai (and thus it was in his vision) or referring to the statue of Glutko's head.