* BadExportForYou: The series had a god-awful treatment in Europe. For starters, [[NoExportForYou Episode I wasn't even released]] but, in one of the most baffling publishing decisions in a genre popular in Europe for its baffling publishing decisions, Episode II WAS released. And in a really neat, almost-collector edition-level packaging. Too bad it was only (badly) translated into French and German (in a time when Spanish and Italian translations were already common place) and with one of the worst 50Hz conversions in the entire 6th Console Generation, which is saying something. As for the plot, the game included a DVD with a few hours worth of cutscenes from Episode I to put European audiences up to speed... sort of, since it barely counted as a barebones version of the plot of the first game. The game obviously flopped hard, so Episode III wasn't even considered for an European release.
* CrossDressingVoices: Jr. is voiced by Bridanne Siddall. In a much more minor example, Creator/WendeeLee voiced kid Gaignun in ''Episode III''.
* ExecutiveMeddling: Numerous - the main brains behind the series were axed by the time the third game came out. The radically different ''Episode II'' was a result of this trope as well, which pretty much led to the series being reduced from six games to three. Ironically, the third game seems to be the most true to its spiritual predecessor and is generally regarded as the best in the series.
* FranchiseKiller: The series was meant to span six games (not counting spin offs)... ''Episode II'' sure fixed that.
* NoBudget: ''Episode III'' seemed to suffer from this. Full CG cutscenes were used only for action scenes, many actors were reused in the dubbing, some cutscenes have extensive slowdown and there were more than a few questionably translated lines. This game was also made during the time that Namco was being bought by and merged with Bandai, so money was likely spread more thin than usual.
* NoExportForYou: ''Xenosaga I&II'', ''Pied Piper'', ''Xenosaga Freaks'', and ''A Missing Year''.
** The dub of ''Xenosaga The Animation'' was done by Creator/ADVFilms in Texas, so no one kept the voices they had in-game. The Japanese dub of the entire collective franchise managed to keep pretty much everyone who was assigned to that character from the start. Creator/RichardEpcar, the voice of Ziggy through all three games, stated that he didn't even know there was an anime, or that it was being dubbed in Texas. Otherwise, he would have flown over there from California and auditioned for Ziggy.
** The Japanese track of ''Xenosaga the Animation'' also had several cast replacements.
*** Creator/MasakazuMorita replaces Creator/TomokazuSeki for Luis Virgil.
*** Creator/TaitenKusunoki replaces Creator/JojiNakata for Marguilis.
*** Hiroaki Miura replaces Creator/TakehitoKoyasu for Tony.
*** Creator/WakanaYamazaki replaces Creator/ErikoHara and Creator/YumiTakada for Pellegri and Shelley Godwin, respectively.
*** Kohei Fukuhara replaces Nobuhiko Kazama for Vanderkam.
*** Creator/YasuhiroTakato replaces Creator/TaikiMatsuno for Hammer.
*** Creator/KenjiNomura replaces Creator/UnshoIshizuka for Captain Matthews.
*** Creator/RyokoShiraishi replaces Creator/RieKugimiya for Mary Godwin.
*** Creator/HikaruMidorikawa replaces Creator/NobuyukiHiyama for Wilhelm.
*** Creator/TetsuInada replaces Masaru Ikeda for Helmer.
*** Miho Saiki replaces Eriko Fujimaki for Lapis Roman.
* TalkingToHimself: Creator/CrispinFreeman as Albedo and Nigredo/Gaignun has several instances of this.
* WhatCouldHaveBeen: The story was originally going to be very different for Xenosaga II and III before ExecutiveMeddling caused the scenario writer Soraya Saga to be dismissed and the original script by Takahashi to be discarded. A portion of the old script was retained for the Pied Piper cellphone game. Among some of the things that were originally planned to happen for Episode II:
** Citrine would reunite with her URTV siblings.
** Shion's past history with Febronia.
** Junior rapidly growing to an adult with both options available during battle.
** The ghost of old Miltia.
** The death of Sakura.
** Brief reunion between the URTVS and grown-up Citrine.
** Gaignun vs the Zohar emulators.
** Junior and Albedo vs U-DO vs KOS-MOS 3rd armament.
** Shion's spiritual seeking/witnessing/awakening.
** The truth about KOS-MOS
** Conversation between chaos and the Red Testament.
** Conversation between Nephilim and Abel.
** An antimatter annihilation of Albedo.
** A grand majority of the series was eventually edited out. On top of the series originally being six titles long, the WhatCouldHaveBeen page itself mentions that the series took up Chapters 2 and 5 of the original ideas, with Chapter 1 being the prologue scenes to Episode I. There's also a list on a [[https://web.archive.org/web/20111121075025/http://forums.xgam.org/index.php?showtopic=9137 Xenogears fan forum (spoilers beware)]] of things that could have been but were either put in later in the series or scrapped altogether when Soraya Saga left. For example, ''Jr. was supposed to grow up and have his adult form available in battle,'' as well as something called "Gaignun vs. the Zohar Emulators."
** Several potentially awesome scenes were removed from the scripts of all three games, some being added in later, but not when they were originally supposed to be; and some were completely forgotten about. The most obvious example being the fight between Jin and Margulis, which was in the trailer for the original game but ended up being in Episode II. Another being a potential plot where KOS-MOS eventually got strong enough weapons to destroy a planet, which Shion was supposed to prevent. Also, chaos, the [[spoiler: guy with the ability to destroy the universe, sits around and hangs in the background doing...well, not much. Just shopping and having cryptic conversations most of the time.]]