All Up To You: Will has a large entourage of sidekicks; none of them ever participate in the actual gameplay (until the Fusion Dance at the end), but they manage to show up everywhere Will goes nonetheless.
Anime Hair: The Jackal, of all people, has a blond, spiky, and ridiculously tall hairdo.
Some might have interpreted it as aztician-styled hair ornament, due the readability of the sprite itself.
Anyone Can Die: Subverted when it's revealed that Seth isn't actually dead. Played straight later on, with Hamlet's death being a major surprise.
Artificial Gravity: Seen on the Sky Garden, where you can jump off the edge and wind up walking upside-down on the underside with gravity pulling everything upward.
Artistic License - Biology: The game states that the comet causes rapid evolution by speeding up time, so that organisms mutate faster. However, organisms cannot evolve, only populations — once your chromosomes combine, you're stuck with that DNA. Granted, this could potentially work if it was mutating the organisms, similar to radiation, which is probably the original intent. Of course, in that case, it would not be the biological superweapon the spirits claim it to be, since it's extremely rare for radiation to result in positive mutations.
Another biology fail: The game claims that a camel's hump contains water. It does, in the sense that all organic matter does, but it's a storehouse for fat.
Atlantis: Actually Mu Continent, the Pacific Ocean equivalent. The developers were found of depicting Mu in their games; it appears again as a side quest in Terranigma.
Back for the Dead: Hamlet, who was left behind in Edward Castle when Kara ran away with Will, unexpectedly turns up much later in the game and accompanies what's left of the party to the next destination, an impoverished village that has lost many to the labor trade. He ends up performing a Heroic Sacrifice to prevent the remaining villagers from starving.
Beta Couple: Lance and Lilly. A subplot features their relationship blossoming, which gives Will reason to go to the Great Wall Of China when Lilly temporarily abandons the group after Lance confesses his feelings to her.
Big Bad: Dark Gaia, the malevolent entity using the comet for its own ends and Gaia's antithesis.
Bittersweet Ending: As foreshadowed earlier in the game, the comet's light has an unnatural effect on the evolution of the planet itself. By defeating Dark Gaia, Will and Kara stop the cycle of destruction, enabling the world to assume its proper shape (real-life, modern-day Earth of the 1990s). Will and Kara go there to live new lives, with no memory of their adventures or feelings for each other. Happily, Will and Kara vow before returning to Earth to find each other - and the final scene of the game shows Will, Kara, Lance, Erik, and even Seth (but not Lilly, for some reason) together again, in a modern-day school.
Black Knight: Will is the Knight Of Darkness, but his Freedan form is a more direct embodiment of the trope, being a broad-shouldered knight in strong, black armour with a broad sword and long, flowing blonde hair. A subversion of the current use of the trope, though not as originally written in ancient legend, since Will is the hero.
There's this thing called context, and the translators had no clue about it. No clue if the subject of a sentence is singular or plural, no clue if a character is speaking aloud or thinking to themselves, sometimes no clue who's doing the speaking. Some more accurate translations in areas containing particularly bad grammar (as well as the censorship issues encountered in Bowdlerise) can be found here http://www.terraearth.com/illusion-of-gaia/translations/.
There are more than a few proofreading fails, like when Kara is referred Karen (as she was in draft of the translation seen in the beta,) or the spot where "violinist" was misinterpreted as "violent".
Blond Guys Are Evil: King Edward is implied to be a less than benevolent ruler who gladly makes use of his power to invade other countries. There's also the fact that he's willing to have a child thrown in jail for not bringing him what he asked for. Oh, and we also have the Jackal, a ruthless mercenary who spends nearly the entire game chasing after Kara on her father's orders.
Bonus Boss: Solid Arm, a.k.a. Metal Mantis, the first boss from Soul Blazer, the true form of Gem the Jeweler.
Book Ends: The game begins and ends with a scene of the hero and his friends at school.
Boss Rush: The end of the game forces you to fight every boss you've faced so far in succession, though you can still heal and save after a couple of them. At least the earlier ones are easier now that you're (a) using Shadow, (b) more powerful and carrying more health, and (c) presumably better at the game than you were when you first fought them all.
Bowdlerise: Slaves are never called slaves, they are laborers or servants instead. References to the cannibal tribe eating people were written out to the point that players might not suspect they're a cannibal tribe. Most suggestions of polytheism are obscured.
Kara: "It's as if we've become spiritsnote gods..."
Bragging Rights Reward: You gain absolutely nothing for collecting all 50 red jewels aside from access to the Bonus Dungeon and its Bonus Boss. Oh, and you have to fight him using Will (instead of the stronger Freedan or Shadow) so it's probably a longer fight than most of the others put together.
Calling Card: The Jackal carves a picture of a...well, a jackal, to mark the places where he's been.
Catch a Falling Star: Double-subverted. Neil uses his airplane to save Will from freefall, but only on the second pass.
Chekhov's Gun: An NPC in the Pyramid tells you that the hieroglyphics room is rigged with a sound-triggering booby trap. Just before that level's boss fight, Will sets off this trap by playing his flute, killing the Jackal who had taken Kara prisoner.
The Rainbow Speak also works like this with character speech. Will's text is yellow, Kara's is pink, Lance's is green, Lilly's is blue, Erik's is orange, Seth's is purple, and Neil's is gray. Everything else uses white text.
Controllable Helplessness: There's nothing you can do to get out of the prison cell in Edward Castle faster, even though you can walk around and examine things. The same is true of the shipwreck sequence.
Corrupt Corporate Executive: To say that Rolek engages in shady activities is to say that the ocean is damp. That said, it may be because Neil's parents were replaced with demons.
Crapsaccharine World: On the surface it's a typical 90s JRPG, all bright colors and friendly neighbors, but there's impending doomsday, famine, slavery, and human trafficking lurking around every dark corner. Pointed out in-game that the nicest looking towns tend to have the seediest underbellies.
Difficulty By Region: In the Japanese version, herbs fully recover your health. Also, you don't have to attack the first boss's hands to hurt him, and the earthquake attack can be used to stun a boss.
Difficulty Spike: Mu, where the blobs and skeletons of previous levels are suddenly and unexpectedly replaced by rock-hard enemies that can become temporarily invincible, teleporting monsters with homing shots, a water depth puzzle, and a particularly difficultDual Boss. Ankor (sic) Wat is another spike, though mercifully there isn't a boss at the end of it.
Dwindling Party: A (mostly) non-fatal version. Will's group grows to six members at some points, but they leave one or two at a time as the game nears its conclusion.
Dream Melody: Will has his grandmother's lullaby, which turns out to be the key to revealing her village of origin and an identifying call. Also, a couple dungeons have background music that turn out to be versions of other melodies.
Earth All Along: After defeating the comet, the world assumes its natural shape, which is that of present-day Earth.
Easy Amnesia: Lance suffers this after a shipwreck. His family has bad luck with this, as his missing father turns up half a world away with Identity Amnesia courtesy of a different shipwreck.
Eleventh Hour Superpower: The Firebird ability from Will's Fusion Dance, as well as the ability to travel into space to stop the comet.
End of an Age: As the spirit of Angkor Wat foretold, Will is destined to usher in the modern, industrialized world. He has mixed feelings about leaving the world as he knows it, and players will likely sympathize with the fantasy world giving way to life as we know it. The closing narration points out that the new world may not be as open or as wild, but it has good people in it, and that makes it worthwhile.
Expy: The Flasher enemies that appear in Mu are pretty much identical to the Wizzrobe enemies in the Legend of Zelda series, attack pattern and all.
Family-Unfriendly Death: Hamlet, then later the Jackal, both of which get burned alive. The latter's is particularly gruesome.
Fetch Quest: The journey to Mt. Kress is one of these, as there's nothing about the quest or its objective that seems relevant to finding Mystic Statues or advancing to new areas. And when you do advance, you wind up going to Ankor Wat on another fetch quest... only this time the game doesn't even tell you that it's a fetch quest.
Gameplay and Story Integration: The scene where Will is trapped on a raft. He gradually gets more and more hungry and the narrative tells us that Will's feeling weak from hunger. Look up at his health and you'll see that he's gradually losing health, too.
Genius Loci: The game appears to subscribe the the Gaia Hypothesis concept of the Earth as a living organism. Organisms exposed the the comet's light mutate, and the Earth is no exception. This ends up being the explanation for why the game world is unlike the real Earth.
Giant Space Flea from Nowhere: Bosses seldom have much in the way of context. The major exceptions are the vampires and the final boss, who are discussed quite a bit in advance of their actual appearances.
Sand Fanger is mentioned ahead of time if you happen to talk to the right NPC in Watermia, though it's described more as a dangerous beast than a malevolent antagonist.
The red jewel in the fisherman's pot is a double example; the manual has a guide, which tells you that's where the jewel is, but it fails to mention the condition for the pot appearing — it's randomly decided each time you enter the area.
Humans Are Bastards: The game occasionally likes to remind you that humans destroy the environment, mercilessly kill each other, and think themselves superior to giant man-eating fish. Furthermore, while the ending does show you saving the human race, it does take pains to remind you that "(T)he Earth was the only one that looked sad."
Inventory Management Puzzle: Will can carry no more than sixteen items, and as you fill those slots with precious, finite Herbs, freeing up space for new quest items gets tricky late in the game. The 50 Red Jewels seem like a headache waiting to happen, but fortunately they can be sent off to the Jeweler at any time.
Invisible to Normals: Itory Village is like this, invisible to the human eye until a song from the village is sung (or played on a flute, in Will's case.)
Jews Love to Argue: Rofsky and Erasquez, those Einstein-looking old men in Euro, are supposed to bicker and trade insults with each other but the translation butchered their dialogue even worse than it usually does.
Kid Hero: All of the protagonists appear to be in the neighborhood of 12-15 years old. Will is a bit taller than his friends, so presumably he is a little older, but definitely no older than 15. Will's cousin Neil is the only exception, appearing to be in his late teens or early twenties.
Lilly celebrates her 15th birthday at one point in the game, so it can be assumed that the ages of the other kids are in that area. Erik is likely the youngest, and Will is just a tad taller, so possibly older.
Landmark of Lore: The game's dungeons include real locations like Angkor Wat, Nazca, the Great Wall of China, and the Great Pyramid, as well as mythological locations such as Mu and the Tower of Babel.
Laser-Guided Karma: It's implied that many of the comet's victims were horrible people who effectively lost their own souls through their evil deeds. Case in point, Neil's parents, who have been using their company as a front for the slave trade in Euro.
Law of 100: Collect 100 DP to earn an extra life (up to 9), allowing you to respawn in the same room when you die (albeit not at full HP).
Lost Forever: The game's highly structured plot results in several points where the characters take one-way trans-ocean trips, making backtracking to collect items you might have missed (mostly those Red Jewels) impossible. The last of these occurs around the midpoint of the game, so after that you can actually skip something and go back for it.
Love at First Note: Grandpa Bill mentions that this is how he fell in love with Grandma Lola.
Ma'am Shock: Queen Edwina is appalled when Will innocently refers to her this way. Not the most polite way to address a queen, Will...
The Maze: Mountain Temple. The manual even suggests drawing a map as you explore the area.
Message in a Bottle: Will and Kara find one...while adrift at sea themselves. You eventually get a chance to help the people who wrote the note when you storm the Diamond Mine and set them free. In return, they give you a healing song (for Lance's memories).
Organic Technology: The endgame reveals that the comet is a Lost Super Weapon created by an ancient civilization that mastered biotechnology and altered organisms to suit their needs. Shadow is another one of their products.
Our Angels Are Different: A whole colony of them live in a secluded place underground. They apparently die if exposed to sunlight for too long, and they're rumored to be the form into which humans will evolve.
Palette Swap: Most enemies have more powerful versions with a different colour scheme (and sometimes different attacks), but it's most noticeable in the Sky Garden. There, every enemy on the underside is a tougher Palette Swap of those on the overside.
Phantom Zone Picture: Ishtar's paintings are lovely to behold, but have the unfortunate side effect of trapping their models inside them.
Princesses Prefer Pink: Kara seems to be a particularly egregious example of this trope, seeing as both of her parents wear blue.
Put on a Bus: Seth, who disappears abruptly when a giant sea creature attacks the Ghost Ship. He does reappear briefly later on, but in dialogue only, as he transformed into the same creature that sank the ship. Eventually, all the characters leave the party forever, and only Will and Kara see the quest through to its end.
Psychic Powers: Will's friends make a big deal out of his telekinetic powers early on. He also has some sort of ill-defined, seldom used predictive power that serves as a red flag in the Russian Glass game, and makes whatever wire you pick to disarm a bomb automatically correct.
Rainbow Speak: Every named character speaks in a text color different from the default blue-white text, as do a few nameless, but prominent, characters. The color of the speech text also largely depends on the character in question.
Ransacked Room: After Will and Kara escape from Edward Castle, they return to South Cape to find Will's entire house completely trashed.
Rebellious Princess: Kara, who appears to have made several unsuccessful attempts to run away from Edward Castle before the start of the story.
Regional Bonus: Beyond the increased difficulty, the international versions of the game have bug-fixes and graphics alterations. Some are for Bowdlerization purposes, but others add flavor to the game. For instance, the second boss went from run-of-the-mill giant bird to winged Babylonian-style statue.
The Sacred Darkness: Will's powers use Gaia's "Dark Energy", and there are no negative connotations associated with them. Not that there aren't bad darkness powers; the Final Boss is called "Dark Gaia".
Schrödinger's Gun: When presented with multiple choices, Will guesses correctly thanks to his psychic powers. No matter what option the player picks, the outcome is the same.
Early in the game, Will is asked to pick a card. No matter what the player picks, it is the right one.
Later in the game there is a Wire Dilemma, but both wires are the right one. The bomb only explodes if the timer runs out and you haven't beaten the accompanying Dual Boss yet.
The Russian Glass game does have a wrong answer, but you're given a chance to back out if you try it, unlike the safe glasses.
The Skeleton head enemy from ActRaiser is in Angel Village.
The Moon Tribe looks like a spirit enemy from Soul Blazer.
Just watch a Let's Play of ActRaiser and count the number of enemies, themes, and other such goodies that were later used in Illusion of Gaia. For example, a statue that is somehow connected to a Crystal Dragon Jesus and its form being used to get through a level. Heck, even many of the sound effects are re-used between this game, ActRaiser, Soul Blazer, and Terranigma.
Show, Don't Tell: Will narrates the story in some of the more plot-heavy bits, but the translation has an unfortunate habit of turning his narration into dialogue and his dialogue into narration. It's particularly confounding in the raft sequence, in which it magnifies the Strangled by the Red String aspect of Will and Kara's romantic relationship.
The unintended Strangled by the Red String thing continues into the ending, where lines that were meant to refer to Will and Kara's Reincarnation Romance continuing into the future were misinterpreted as referring to their meeting at the beginning of the game, when neither of them found anything interesting about each other.
Supreme Chef: Grandma Lola, probably - as often, the translation is inconsistent. Foreign Queasine is also involved. Her signature dish is snail pie, but Will thinks it smells delicious and Grandpa Bill ate four slices. On the other hand, she made some soldiers sick with a different pie, so it could be that she's a Lethal Chef and Grandpa Bill just has very unusual tastes.
Taken for Granite: An effect of exposure to the comet encountered in the Natives' Village (and referenced in Mu).
Team Pet: Hamlet, Kara's preternaturally smart pet pig.
Took a Shortcut: Muggle secondary characters can and will show up wherever the plot demands, no matter what extraordinary abilities Will has to use to achieve the same results. One of the kids that is established as being rather weak (both physically and mentally) is able to walk in through the very same door that Will had to use spin-dash jumps to reach. Lilly, at least, can turn into a dandelion seed and drift past any danger; but the others have no such capabilities.
The Unfought: The Jackal. He's killed by a booby trap triggered by Will's flute in a cut-scene just before the actual boss battle of the Egyptian temple.
Urban Segregation: The town of Freejia, with a well-to-do neighborhood facing the road... and a very poor slum and a slave market on the other side.
Video Game Cruelty Potential: You want all the Red Jewels? Hope you're okay with telling a slave-trader where his escaped slave is hiding. At least you can take comfort in knowing that you'll soon break into the slave camp and free all the slaves, presumably including the one you turned in.
Waiting Puzzle: A puzzle early on has elements of this. One room in the Larai Cliffs has a floor of gold tiles, and when Will plays his flute, one tile glows. Will must then stand on that tile for several seconds before a door opens in the southern wall.
We Hardly Knew Ye: Seth, who is left behind in South Cape with Lance and Erik until all three suddenly show up on the Incan Gold Ship, then apparently gets eaten by the giant sea monster that destroys the ship. He's not exactly dead, though, having turned into the same sort of sea monster. He's eventually able to communicate a message to the party explaining that this means he cannot return to them.