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.
Better Than Canon: Due to a translation error, the game implies that Yui defeated Citan in a sword duel, and they fell in love when he was recovering from the fight. This isn't true, according to Perfect Works, but a lot of fans want it to be true.
Big Lipped Alligator Moment: Several, but the most notable comes in Shevat. Maria learns that her father is all but dead and is confronting the fact that she will have to fight his last creation, which speaks with his voice, when who shows up? Yep, Chu-Chu, the Hello Kittyreject, to inflate to gear size and engage a scripted battle that is impossible to lose, managing to provide neither challenging gameplay nor story development. Ewoks built a battleship out of twigs and fought the death star for five minutes, almost winning then inevitably failing, just for lulz.
Complete Monster: Miang is eventually revealed to be the game's true Big Bad. Initially Ramsus's wallflower assistant, Miang turns out to be an ancient being with one goal: to prepare humanity for harvest by Deus. The 'Eve' of the world, its first woman, Miang has helped to manipulate human history by running an Ancient Conspiracy, causing countless wars and conflicts with countless deaths. Miang demonstrates nothing less than cruel satisfaction at her manipulations, rubbing it in her lover Ramsus's face how he was a failed prototype of Ramsus's rival Fei to break his already fragile mind. Miang awakens Deus and causes the genocide of almost all humanity, in addition to having made it her personal mission to destroy the happiness of lover Fei and Elly's past incarnations every time they reincarnate. Only Miang demonstrates such sadistic cruelty in her job in Xenogears.
Fanon: The strategy guide gives Emeralda's the surname "Kasim" after her "father", Kim Kasim. Official materials don't usually follow suit. Fan materials, however, frequently do. Probably because the other official materials aren't available outside of Japan.
Most jarringly, if ironically easy to miss, the Ethos is structured like and has symbols similar to those of Christianity, especially the Catholic Church, with confessionals, cross-like shapes, and bishops. In its theology, however, it is completely lacking a historical Messiah figure and due to that has more in common with Judaism or Islam, doctrinally speaking, than with Christianity, meaning all those crosses, habit-wearing nuns, cassock-wearing priests, and hierarchical/practical similarities to the world's largest Christian church are misplaced, sometimes severely. The most blatant of these loosely-Christian references is a scene with three crosses on a hill with a name very similar to "Golgotha", the Hebrew name for the hill where Jesus was crucified; but even the most Messiah-like figure in the game (from a Gnostic-type religion, not from Ethos) didn't die by Crucifixion or anything remotely like it.
Also, the scene where a giant, fluffy, pink mouse is crucified. No, seriously.
All of the pixellated nudity— even if the character designs make you think you'd want to see it, it's really not exciting. At all.
The implied Chu-Chu orgy in Shevat qualifies too, though that one takes Fan Disservice to horrifying levels.
Freud Was Right: Vanderkaum really likes his cannon, and Bart really loves his Bart Missiles and the cannon on Ft. Jasper. Elhaym was originally created by seven-year-old Abel's desire for a "mother's will". The two become lovers, for over 10,000 years. All of this was completely intentional, as the game was partially based on Freud's works.
Gamebreaker: For much of the first disc, Vierge + Ether Doubler + Power Magic = one shotting bosses with Aerods. Ether Doubler does exactly what it sounds like: doubles the power of any Ether attack, at the expense of also doubling the EP cost. What makes this combo truly broken is that Aerods don't have an EP cost; they're powered by Fuel. Thus, they get massively buffed by Ether Doubler for free. A bit later you get the Power Crisis which causes the user to deal more damage at lower HP - except it's a bit too effective, losing even a few HP makes the user the most powerful attacker in the game and at low HP you can kill a gear sized enemy on foot.
The Holy Pendant doubles the duration of in-battle effects on the equipped character. Possibly due to a programming oversight, this bonus also extends to Gear combat, which means that the equipped character can spend up to six turns in Hyper Mode. Miss your chance to buy one? Never fear! You get one for free when Billy joins you.
More generally: Citan is obscenely powerful, due to his high HP and the highest Agility stat in the game. The Power Crisis accessory is obscenely powerful, due to increasing the equipped character's attack power by huge margins as their HP gets lower. Equip Citan with Power Crisis, let him get hurt, and you have an unstoppable death machine on your hands. And just in case you don't think he's broken enough, later on he gets his sword.
Equipping Elly with three Power Magics and using Aerods (or ether) is less of a nuke than an Ether Doubler, but they aren't Lost Forever and are the optimal alternative. Most bosses can be taken down after four or five hits with Aerods on Power Magics, at least while Elly's still in the party.
Adult Emeralda, especially if minimize your usage of her prior to the adult transformation (so as to maximize the number of level-ups she can get as an adult). She gets a hidden 20% bonus to both physical and Ether attacks, she's got the second best Agility after Citan, and all of her other stats will boost for every single level-up, including unusually good HP gains. While her starting HP isn't very good, it doesn't take her long for the fast growth to make up for it, she has the best Ether abilities in the game and she's top 3 in physical power. She combines all of the best traits of Fei and Elly. Not a coincidence, given that their previous incarnations created her.
Bart's "Wild Smile" ability qualifies, due to the fact that in can affect most bosses. The effects also stack, so while one casting results in "enemy usually misses", two or three means "can't hit the broadside of a barn". He also already knows it as soon as he joins up and the game has a way of telling you that you'd better use it if you want to live by making the first boss after Bart joins nearly impossible to defeat without using it on him.
Good Bad Translation: See Better Than Canon. While the line about Yui beating Citan and falling in love with him while he's recovering is actually a mistranslation (according to Perfect Works), it's widely considered an awesome story element and is well-enshrined in the fandom by now.
Iron Woobie: You'd never know how much childhood trauma Bart went through if Margie didn't tell you.
Love It or Hate It: You'll either hate this game or love it. However, it'll take at least one playthrough, mild knowledge of gnosticism, and a gander at Perfect Works to even come close to understanding it.
The Elements. In particular, Tolone and Seraphita are never seen outside each other's company.
Miang admiring Elly's beautiful eyes before hypnotizing her has been noticed by the fandom.
Mary Sue: The amount of intricate planning that seems nigh-impossible to fully flesh out, plus the fact that he never loses and in fact gets exactly what he wants in the end, despite every horrible thing he took plart in, AND just gets forgiven by Fei and Elly in the end, Krelian can honestly come off as very much like a particular type of Mary Sue.
Miang, possibly. While she did do the on-the-ground work while Krelian was plotting from on high, some people consider her less badass because she was a direct creation of God instead of a badass who built his own powers.
Memetic Molester: While Miang's experiments as Karen are stated in the story to be for the purpose of finding the Contact, one can't help but wonder whether some of the probing she did to Fei as a child was really necessary...
And on top of that, she comments on how "handsome" Fei is when he participates in the martial arts tournament, knowing that he's that same child who grew up.
Elly! Miang saves her from Dominia's wrath, only to get alone in a room with the Gebler-officer-turned-traitor and... admire Elly's eyes before hypnotizing her. We know about Miang's "arrangement's" to sabotage the Yggdrasil's engines using Elly, but were those the only ones?
Mondegreen: From "Knight of Fire", a lot of people hear something like sex in the gas chamber being sung in the background.
Dan. The Dark Id had a field day with mocking him.
Hammer is a more controversial case. Is he endearing or annoying? Are his MAD SKILLZNarm or Narm Charm? Is he a Byronic Hero or a Complete Monster? Is he a cold-blooded murderer or was he not responsible for his actions? Hammer is intentionally written as sympathetic character who is loved and morally exonerated in the eyes of Elly and Rico. Audience reaction to Hammer, however, varies wildly; the audience may love him throughout, or start hating him after his (legitimately shocking) betrayal (and then, may or may not forgive him after his demise), or they may have hated him from the get go.
Krelian himself has to be the most hotly debated character even to this day. The man was personally responsible for countless numbers of people suffering and dying and was directly responsible to most, if not all the events of the game. Many people will often call BS on how Fei and Elly so easily forgive him in the end.
That One Level: The Tower of Babel — this one takes some explanation.. are you sitting comfortably? Good, let's begin:
The Tower of Babel is entirely made up of long jumping puzzle segments, and is entirely vertical: if you fall, you end up falling all the way to the bottom. The platforming controls, on a good day, are abysmal and unresponsive. Strike one.
When a random battle is triggered in Xenogears, things happen in sort of a strange order: Instead of going to a loading screen, or hiding loading using the battle transition, the game begins loading (you can hear the Playstation spinning up) but it's a few seconds before the battle actually starts. During this time you can move around as normal on the world screen. During this "loading time", although you can move around, you can't jump, so you end up walking off the ends of platforms. The Tower of Babel has a pretty high monster encounter rate and lots of ends of platforms. Strike two.
The camera only has a few angles you can look at it from. Not every platform in the Tower of Babil is aligned with these camera angles, making it extremely difficult to line up the jumps you can make. Strike three, and you're Scrappy.
As a final insult, you spend the entire level in your Gears, which have the ability to fly. After finishing the jumping portion of the dungeon, you see a short cutscene which is introduced by the Gears flying a few hundred feet to get to the final area of the tower.
The Rope of Robots thumbnail theatre is really not exaggerating the reactions people have to this damn level.Some of these quotes (scroll down, you'll know it when you see it) were uttered by this troper and their friends over the course of the hideously long climb. It's really that bad. (ASS ASS ASS AAAAAAAAAASS)
The last dungeon of the first disc is this to some players, if only for its sheer length; it goes on longer than the Kislev Sewers and the Tower of Babel COMBINED. To be fair, this is technically because it's two dungeons (Soylent System and Krelian's Lab) linked together. Making it even more annoying is that nearly every enemy has absurd Ether Defense. This hurts when Elly is one of your required characters.
The final dungeon as well. The game even gives you maps of the place. THEY DO NOT HELP.
That One Boss: Redrum! Instant kills (that heal him!), area wide damage (that also heals him!), a ton of negative status ailments, and the highest HP of any boss fought up to this point by far.
Miang and Opiomorph if you don't know what you're doing.
When you do know what you're doing, Opiomorph just takes a really, really long amount of time to beat.
Id in Zeboim certainly qualifies. He attacks multiple times in one turn and is so strong he can kill most party members in one or two attacks. He also likes to dodge your Deathblows.
What Could Have Been: The Xenogears Perfect Works makes the game look like it wasn't nearly long enough to complete the story the designers wanted, as shown by Xenogears being "Episode V" out of at least VI. Though the notes about Episode I "Era of Interplanetary War" has similarities with the later made (but earlier on the timeline) Xenosaga series, so the episodic format was most likely dropped.