The main character is a female who wears a very modest and practical dress for the entirety of the game, which by itself is like a subversion apocalypse. Though her naive optimism is picked apart throughout the first half of the game, instead of discarding her ideals she matures them instead into something practical yet still optimistic.
Magic doesn't expend MP; rather, each character has a "Force Gauge" that builds as they attack, with spells becoming accessible when it reaches a certain level.
Characters don't buy new weapons: they upgrade and customize their existing ones.
You can't buy healing items. Since Filgaia is a wasteland and all the healing items are fruit, healing items are incredibly rare, forcing you to rely on healing spells in battle and a limited Vitality Gauge, which will keep your health topped up for a time. You later get the ability to grow your own healing items, but just like real gardening it's a long and patient process.
You can use an item to rename almost any NPC or ability in the game.
You can't see items or places on the world map automatically. Instead, you have to search for them using a radar-like ping. This includes towns and dungeons.
Although there are random encounters, there's a "migrant seal" system which allows you to skip encounters if you wish, or even bypass them entirely if you're overleveled.
An interesting tidbit - this game was the first not to be localized by Sony. Squaresoft, of Final Fantasy fame, performed the localization process, which was noticeably of much higher quality than the Blind Idiot Translations of the first two. Unfortunately, this also created some continuity errors with certain names that were intended to be references to the first two games. Future entries were handled by XSEED (and in onecase, Agetec).
This game provides examples of:
After the End: Filgaia was turned into a desert wasteland by a cataclysmic event that actually only happened about ten years ago, but also erased everyone's memory of it happening, so they think it was in the distant past.
Armor-Piercing Slap: Virginia gets this treatment not only once but twice. First by her uncle, who slaps her because she tried to be a hero and could easily got herself killed (well, rushing in a dungeon filled with goblin smugglers, all alone at level 1, isn't the brightest idea, especially when you're The Chick). The second time by Maya, a Drifter like her (but way more experienced), who gives her a What the Hell, Hero? speech after Virginia tried to pursue the antagonists and nearly got herself killed, save for the intervention of her comrade Jet, who she completely ignored while he just saved her life. She quickly realized how naive and stupid she acted this time, thanks to Maya's speech.
And there's the time where Virginia slaps Maya...only to see that she blocked the slap with her arm. Then Virginia forces and reach Maya's cheek.
Awesome McCoolname: Gallows Carradine. Honestly, the Wild ARMs series is in love with this trope.
Bag of Sharing: Especially ridiculous in the prologue, which shares items between characters who haven't even met yet, with the items traveling back in time if you choose to play the four prologues out of chronological order. One of the few outright weird Fridge Logic moments in the game.
BFG: The gun mounted on the sandcraft, which can do a million points of damage in a single attack.
Bittersweet Ending: While Siegfried and Beatrice are both defeated, Filgaia is still a wasteland. The leader of Filgaia's most prominent religion is dead, and the heroes are blamed for his death. On the other hand, the party isn't too broken up about it, and the ending sends the player off with an uplifting feeling; after all, it's not like people haven't tried to kill them before. The last thing we see is that Hope Springs Eternal.
Bolivian Army Ending: Subverted during The Stinger, as the heroes are shown to have come out alive and unharmed, though everyone thinks they killed the guy who headed Filgaia's biggest religion.
Brutal Bonus Level: One hundred floors. No save points whatsoever. Bonus Boss from hell, Ragu O Ragla, waiting for you at the end. You have to fight him twice. In. A. Row. And he is even stronger the second time around. Have fun!
Catchphrase: Janus is "just trying to do things efficiently."
Chekhov's Gunman: One in particular stands out, spanning the entire damn game. Beatrice, the final boss, shows up in the first ten minutes, and repeatedly shows up for small portions of cutscenes throughout the game as an almost unnoticeable side character until she reveals herself as the Woman behind the Man who was behind 3 People who were behind One Man. Yes.
On the slightly saner level, the statue that is Asgard, Janus' ability to split his body into multiple forms, the four extra shrines at the Southern Temple, and Hyades. There's a bit going on in this game.
Crew of One: Subverted, the sandcraft requires four crew members to be used, each in different jobs roughly corresponding to actual ship jobs- Helmsman, Gunner, etc.
Cybernetics Eat Your Soul" The Metal Demons are a weird version of this; it's stated pretty clearly that it was after they became monsters that they took up cybernetics, but averted in the case of the heroes ARMs, which are stated to be usable only because of the everpresent nanobots in soil, air and the heroes themselves.
Death World: The state of Filgaia in this game is the absolute lowest in the entire series.
Disc One Final Boss: Happens several times, actually; Virginia and her team fight what appears to be their ultimate nemesis and defeat him/them only to find an even bigger threat looming on the horizon. Interestingly, the intro movie continues to change throughout the game to reflect this. The game feels very much like several seasons of a multi-arc anime because of this.
Evil Laugh: Once the antagonists (with the exception of the really dangerous ones) begin to lose it, you will hear them laughing out loud like mad men quite often.
Evolving Credits: Another series tradition. The "outro" for when you quit the game after saving shows a beautiful scene, with a sung score, detailing the party's level, stats, and equipment as scenes of Virginia's life slowly drift by.
Also, uniquely, the game has Evolving Intros- the anime opening sequence that plays when you load your save changes depending on storyline changes- villains come and go, major scenes get resolved, etc.
Expy: Maya is an expy of Jane from the first game. Not only are they alike in appearance and personality, they serve as the rival for the resident lead female (romantic for Cecelia, professional for Virginia). Though, its Virginia who takes Jane's surname. This makes sense, since Maya is actually using her power to become any character from a book to literally be Calamity Jane in appearance, personality, and abilities.
Foreshadowing: Everything is foreshadowed. Most of it is obvious, but you'll probably overlook Shane's explanation of his prophetic dreams, which summarizes the entire plot and is the first mention of Beatrice. Since this dream came from Beatrice in the first place, it's the first part of her Gambit Roulette.
For The Cel Of It: One of the earlier examples of cel-shading on the PS2, and highly successful; the look merges well with the Wild West aesthetic.
Gambit Pileup: By the end of the game there are multiple spanners, chess masters, and gambits of all kinds, from Batman to Roulettes, piled up in a giant convoluted mess.
Gatling Good: Maya Schrodinger has one. Mentioned less for the weapon and more for her...interesting means of carrying it.
Also, a Force Ability is named "Gatling", allowing you to perform a barrage of regular attacks.
Guide Dang It: The game never actually tells you how Finest Arts works. Since it's a Game Breaker, this may or may not be deliberate.
The Dark Luceid arcana is a great spell... that is, as long as you know how it works. Nothing in the game tells you, of course. The big secret is that it's damage is affected by the elemental affinities of the target(s), losing power for each weakness, but gaining power if resist it at all (and of course, the greater the resistance, the greater the boost). It'll do next to no damage (or no damage period) on most enemies, since a good chunk of the bestiary has at least one weakness, but for the monsters that resist, nullify, or absorb multiple elements? They will break down and CRY if they see you cast this.
The Gunslinger: Unlike previous Wild ARMs games, which mixed swords and fantasy weapons together, pretty much everyone uses a gun. Everyone in your party wields a different type of gun.
This fact leads to a hysterical scene. The party is opposed by villainous Huskarls, a group of knights equipped solely with swords. The party is flabbergasted that someone would be using a sword in this day and age. When the party kills them deader than disco, the guy who sent the Huskarls after the party freely admits that he thought they'd all get killed, using swords like that.
Jerk with a Heart of Gold: Maya may seem harsh, but besides the obvious motivation of wanting to get rid of other Drifter competitors, she does have a sweet spot for Virginia, protecting her in her own way (and literally saving the party's life at least once). Lampshaded by her own brother, Alfred.
"My sister's a little... you know... She comes off as crass, but she's trying her hardest to be nice."
Last Lousy Point: The Black Box, which requires you to open every single other treasure chest in the world.
Lost Forever: Didn't trigger the events to begin the Telepath Tower sidequest in time? Too bad, no EX File Key for you!
Lost Technology: The Council of Seven was founded to try and revive it, and the one major religion on Filgaia (the Order of the Ark of Destiny) is essentially dedicated to it (even having their headquarters in a millenia-old Generation Ship!).
Meddling Grandmother: Late during the second act, just before going to the last shrine, Halle, Gallows's grandma, outright reveals to her grandson that she had an hidden agenda, and that she intentionally orchestrated the events of the game's beginning, in which she succeeded to bring back home Gallows, and set him up on the rails of his quest and duties (which he ran away from at the beginning of the game).
Mega Manning: Maya Schrodinger can do this by reading comic books.
Mexican Standoff: The "Select a Character" screen is a stand-off between the main characters, and you play through their backstories before the stand-off gets resolved.
New Game+: The EX File Keys, which require doing some insane side quests, are used in a New Game Plus to unlock things. Good luck getting them all.* you only need two to unlock the New Game Plus.
No-Holds-Barred Beatdown: An direct allusion to this trope by Maya Schrödinger, who says this to Virginia immediately after saving her and her party from Asgard (who did OHKO them) : "I, Maya Schrödinger, will crush you to the ground, no holds barred. Just remember that."
Sand Is Water: The oceans are, quite literally, sand. Giant sea monsters live in it, and you have to drive a boat out to fight them. Don't ask.
Sarcastic Clapping: Janus does this to Virginia after she gives him yet another gallant and long-winded speech. Virginia gets furious.
Save Token: Gimel Coins, which can be used to save your game at any time you're not in battle, in addition to town-only Save Points. Gimel Coins allow you to save anywhere, but were not sold in shops. Whatever you found in chests or from the exceptionally rare drops were all you got for the entire game.
Schizo Tech: Fantasy and Wild West Tech, as is common to the series. However, in this game, the latter is played up far more prominently, with the fantasy elements almost removed, arguably improving the game by forcing it to focus on what was unique in Wild ARMs in the first place.
Shout Out: Oh so many, even by Wild Arms standards. Not only do many elements from Wild ARMs 1 hover in a grey area between Expy and straight reappearance, but monsters and locations have a remarkable tendency to reference myth, folklore, and pop culture in one way or another. Norse Mythology and The Ring Cycle get a particular emphasis, from Siegfried to Yggdrasil to Virginia's father and his remarkable resemblance to Odin's mortal disguise.
When Shady, the cat of Maya's group, is trapped, he yells "No more walls !" Add this to the fact that in battle he only has two attacks, with 50% of chances of using each one. And that Maya's family is named "Schrödinger." And that said family's ancestors made Shady completely claustrophobic. Poor Schrödinger's cat.
Took a Shortcut: Martina, an unarmed NPC little girl, somehow travels the world without the use of a horse, sandcraft, or aircraft. Lampshaded several times by the party wondering how the hell she gets to the places she does.
Clive also does this in his prologue, since his starter dungeon can only be reached by air.
Train Job: The introduction of the game begins with all four party characters meeting each other performing the same train job... and interfering with some villains who have also come to perform the same train job. It was a very busy train that night.