These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alex's status as a villain actually is somewhat contentious, as it isn't until after the second game ends that it is revealed that he had an ulterior motive for wanting the lighthouses lit. Which is something that Saturos and Menardi—and Felix—were already trying to do when they met him.
The Wise One being a jerk god that wants to keep Alchemy out of human hands for his own selfish reasons.
That last one might have been jossed by Dark Dawn, since it's revealed the Wise One is actually a man-made being and it's outright confirmed that the ancients screwed themselves over and tried to prevent Alchemy's release. However, this just raises the question of whether the ancients were outright Jerkasses when it came to their policies on Alchemy.
Crack Pairing: Everybody x everybody, but the weirdest has to be Isaac x the roof of his house. Yes.
That "weirdest" title might be getting a challenger: the fandom has started shipping literal ships.
Crowning Moment of Awesome: Playing for the first time? Good for you! Found four Venus Djinni yet? Great! Go unset them all and summon Judgement.
The final dungeon. Blasting ice with fire was never so satisfying. Saving the world while doing so? Priceless.
In TLA, the girls and Kraden ganging up on Piers to make him say his age. Piers ends up begging Felix to help... but to his shock and despair, Felix apparently kind of wants to know, too.
A well-hidden Easter Egg: if Felix keeps saying no in the game's various yes/no choices, or just generally disagrees with Kraden for most of the game, when they reach Lemuria, Felix would be ill-advised to say no yet again...
Kraden: "What!? Are you INSANE!? Or maybe you think you're funny? Because you're not! Maybe this whole quest is just a game to you, but it's not to me! Are you bored!? Do you want to go home!? FINE! That's it! Then let's go home!"
When Jenna delivers this priceless line:
Jenna: Can't you stop talking about yourself for one second, Alex?
Not to mention, one of the reasons this game still stands out a bit (other than its timing) was that it actually sounded way different than most Game Boy Advance music, and the Game Boy Advance didn't have very good sound-capabilities at all.
Demonic Spiders: The game, thankfully, doesn't have too many of these...until you get to Anemos Inner Sanctum. Practically everything in there is some form of this, the worst being the Sky Dragons.
Also, the Stone Soldiers are pretty nasty, especially when you find out about their Action Bomb capacities.
The Wonder Birds, which are capable of moving three times per turn (!), have devastating fire psynergy, and can revive fallen enemies. Overlaps with Metal Slime due to the immense amount of XP you can get off them.
Draco in Leather Pants: Averted with Karst - besides the obvious fact of being an Anti-Villain, it seems that nobody actually wanted her to take her revenge on Isaac anyway. The events of the plot are probably also a factor.
Saturos is - as noted on the "Golden Sun Wiki" - very popular in fandom for his charismatic personality, and the revelations about Prox in the sequel made his fanbase even stronger.
Karst, who easily has the most relatable motives and well-developed character of all the duology's antagonists. The Ship Tease with Felix, near the end doesn't hurt either, since so many fanfic writers consciously choose to save her, regardless of whether they actually care that Agatio died with her.
Fan Preferred Couple: "Prox-shipping" is not actually canon (so far as we know, anyway), but it is pretty rare to see Saturos and Menardi paired with anyone but each other in the fandom.
Fan Wank: Due to the numerous hints about Anemos and its legends, many people presume that Sheba came from Anemos and fell from there into Lalivero. The game avoids actually resolving this, however. Even so, some people liked the resulting character development, slight as it was.
Game Breaker: In TLA, Isaac's party can be this if they join overleveled.
The summons. Oh so much. You can very easily breeze through 90% of the first game just abusing summons, ending battles (bosses included) in around 2 turns or less. The downside is that you have to put them on standby after every battle and the game is easy enough without them.
The Spirit Ring, an early game healing item in TLA which, most likely due to an oversight, can be used indefinitely outside of battle, ensuring your party full health between every fight.
The Flash+Shade strategy, which involves using two Djinn that cut damage by 60% and 90% repeatedly. You can pretty much stall infinitely against anything that isn't the Doom Dragon or Dullahan.
Alex as well, though he's a bit more subtle about being a bastard. Moreso with each installment in the series, too.
Memetic Badass: There is a fan forum known as the Temple of Kraden, which the Golden Sun wiki amusingly describes as "[where] Kraden is revered as a god-like figure, although it is reasonably sure that users are joking about their level of devotion to him." Also, the below-mentioned joke about him becoming a playable character.
Memetic Mutation: There were a few fans who preferred Piers' Japanese name, Picard, so they used "Pow pow Picard!" as a rally cry.
Kraden is surprisingly popular within the fanbase. As described by Golden Sun's wiki, it is "an endearing tradition to revere him as a godlike figure with comically extreme devotion." To the point that a popular fan-made name for a Weyard equivalent of Christmas is Kradenmas.
Moral Event Horizon: If it were not for Felix's intervention, Agatio and Karst would have arguably crossed this by killing Isaac and Ivan after they were separated from the rest of their group.
Narm: Boreas may be a strong summon, but that doesn't change the fact that it's basically a giant ice maker.
It's also the most useful summon in the entire first game. Which nets it some Memetic Badassitude, which is just hilarious considering yeah, it's pretty much a giant ice maker.
Replacement Scrappy: A small portion of the fanbase remained convinced that Saturos and Menardi had somehow survived their Disney Villain Death and would return in the second game. Naturally, these fans did not take kindly to the introduction of Agatio and Karst.
Actually, many fans like Karst quite a bit, not least because she has well-rounded motives, or her Ship Tease with Felix. She arguably inverts this trope to become more popular than her sister, Menardi, in a number of circles. Due to the games' renowned weaknesses regarding characterization, Agatio... isn't quite so lucky. While it's not particularly malicious, he's largely uncared for by the fandom due to not being seen as a worthy subtitute for Saturos, and is easily the least-popular antagonist from the original games (and the least popular major character to boot)... Poor, unloved Agatio.
Seinfeld Is Unfunny: Yeah, they look generic now, but consider that when they were originally made, the Game Boy Advance platform was literally months old. For a handheld game, it actually was rather impressive for its time. Not to mention, until next-gen platforms game out, it probably still was the best use of the game boy advance's limited sound hardware.
Shipping: Enough of a developed shipping fandom that pretty much every possible pairing among main characters is covered with its own "____shipping" name, and with copious amounts of Crack Pairings too. The Ship-to-Ship Combat can be truly awe-inspiring, especially between Mudshippers (Isaac/Mia) and Valeshippers (Isaac/Jenna). In fact, the shipping fandom is so ridiculously developed that in some circles, even Original Character ships are named.
Just as an example of how fast GS shipping fandom moves, the Matthew/Karis couple was named "Dawnshipping" within an hour of Dark Dawn being announced.
Saturos from the first game (when you face him for the first time) can be quite a menace to players that are unprepared, mainly due to the fact that he has spells that are more powerful than what the players are used to at the point. His second (and final) battle with him is arguably much worse though, as he brought Menardi to assist him.
Briggs counts as an early game example, as, due to Osenia's layout, he can be fought before encountering a number of dungeons and collecting their Djinni, summons, and items. Needless to say, he's going to smack you upside the head if you're not ready.
That One Attack: Dullahan and Doom Dragon both deserve a special mention for the ability Djinn Storm, which sets all Djinn in the current party into recovery mode (removing the stat bonuses of having them equipped to a character and preventing them from being used for summons). Doom Dragon also has a very infamous attack called Cruel Ruin which hits the entire party, has a base damage of 200, and becomes more powerful depending on how much HP the party has meaning that it does MORE damage to a higher leveled party.
What separates this from Dullahan is that there is no factor that randomly KILLS you. What made Dullahan so hard was that in combination with Djinn Storm, it has Charon that can instant kill you in tandem with just doing damage which means that it doesn't matter if you are fully healed, you are still taking a dead member 50% of the time and maybe even two or three. Then he finishes you off with Formina Sage Fulminous Edge. Cruel Ruin itself is not as dangerous mainly because a sufficiently strong party can stand in the face of it and still come out standing, even with no Djinn set. A level 50 party can completely raze the Doom Dragon without suffering a single death while Dullahan can KO the entire party before you even reach half HP with the same level.
On the other hand, Dullahan can be summon-rushed. Doom Dragon is specifically geared to nerf summon-rush strategies by having separate damage calculations for each of its forms. It really depends on your play style.
Virtually all of Dullahan's attacks are That One Attack: Djinn Storm, which puts every active party member's Djinni in recovery mode; Fulminous Edge, which does huge damage to one party member; Charon, which can easily be a Total Party Kill; Condemn, which is a potential One-Hit Kill; True Collide, which hits hard and restores his health; Bind, which disables one party member's Psynergy...is the Bragging Rights Reward really worth it?
You're going to respect Master Maha after that one. How the hell did he ever finish that thing alone?
To elaborate: The exterior mountain climb of Air's Rock is about as long as any given dungeon up to that point in the second game. Then, the interior exploration of Air's Rock is, in itself, noticeably longer than any other dungeon in either game, barring the Lighthouses and the other elemental rocks. It also relies extensively on a (relatively expensive, compared to other utility spells) Psynergy that requires one of the characters to be in her default class, which means repeatedly shutting down and turning on her Djinn for any player who places her in a more balanced class. This dungeon is early enough in the game that the player only has the first three characters, although it is possible to wait until you have the fourth party member to attempt it.
If you want that fourth party member, however, you'll instead have to fight the Wake Up Call Boss massively underleveled, since he was intended to be fought after Air's Rock.
Visual Effects of Awesome: The Catastrophe Summon; widely regarded as the most visually impressive animation sequence ever produced for a GBA game. View it in all its glory Here.