* AlasPoorScrappy: [[spoiler:Flay, after her emotional breakdown and ensuing RedemptionEqualsDeath.]]
* AmericansHateTingle: Flay is a BaseBreaker bordering on TheScrappy in the west. Not so much in Japan, where she's generally well-liked. Which is ironic since the director had actually thought she'd be the type of character to appeal to Western audiences, but things ended up reversed.
* AuthorsSavingThrow: Attempted in the HD Remaster when Nicol's death is retconned to make [[TheDogShotFirst Kira even less culpable]]. The end result was... [[BrokenBase mixed]].
* BrokenBase: It is a Gundam AU series, after all.
** In the HD Remaster, [[spoiler:Nicol]]'s death was retconned to make it appear largely accidental. In the original, he attacks, his target counters, and he's killed. In the remake, he attacks, his target dodges, and his attack carries him into his target's sword, which kills him. Here's [[http://www.youtube.com/watch?v=fhpmGzNK0aI a comparison video]]. On the other hand, Kira's reaction is certainly a reflexive action in both versions (he's trying to avoid an attack) the only thing that really changes is the position of the weapon. The intent is not changed to make Kira look less guilty, since even in the original situation Kira was not deliberately attacking Nicol.
* BaseBreaker:
** Flay is a polarizing character. She spends much of the first half of the show being a manipulative FillieFatale for a sympathetic-but-unjustified reason, and later attempts to make up for it. Either she was a JerkassWoobie who redeemed herself in the end, or a selfish asshole too wrapped up in her own problems to empathize with anyone else and her later actions were too little too late.
** Lacus, given her status as an idol singer, which some fans feel doesn't fit really well with the series' tone. Her turning out to have a large political clout while being a ''teenage'' idol singer also pushes SuspensionOfDisbelief a little thin even though such role is preferred over an idol. Her worst critics argue that she comes off as a hopelessly naive PuritySue who lucks her way into victory and power. However, there are plenty of people who feel that her portrayal as a Peacecroft-esque alternative political figure works fine, and even some who don't mind the IdolSinger angle.
** Kira himself. Some like Jesus Yamato and think it's excellent growth. Others find him a boring CanonSue.
* CompleteMonster: {{The sociopath}}ic [[FantasticRacism Muruta Azrael]], the [[ANaziByAnyOtherName Nazi-like]] leader of the [[WesternTerrorists terrorist organization]] [[MugglePower Blue Cosmos]], wants to [[FinalSolution kill all]] [[GattacaBabies Coordinators]] (people created via genetic engineering) by [[WeaponsOfMassDestruction any means necessary]] and takes [[LaughingMad unholy delight]] in their wholesale slaughter, making [[BigBad Rau]] [[OmnicidalManiac Le Creuset]] seem [[WoobieDestroyerOfWorlds sympathetic]] . He's also [[HeManWomanHater misogynistic]], [[ManChild childish]], [[SmugSnake smug]], arrogant, condescending, and [[PsychopathicManchild enthusiastically psychotic]]. He believes entirely that his subordinates [[WeHaveReserves are expendable]] and willingly sacrifices millions of them just to see all the Coordinators [[NukeEm burn]]. A SoreLoser and a raging {{hypocrite}} who uses [[PsychoSerum drugs]] and brainwashing to turn children into {{Tykebomb}} {{Super Soldier}}s (referred to as the Extended), while claiming that genetic engineering is a sin (it's heavily implied that this is a case of DrivenByEnvy), Azrael is also TheManBehindTheMan to both the [[{{Eagleland}} Atlantic Federation]] and the Earth Alliance Forces, whom he manages to corrupt with his FantasticRacism, and goes out of his way to make sure that neutral nations are coopted or destroyed. Having started the war by launching a nuclear assault on the Coordinator homeland, Azrael hopes to [[ThereIsNoKillLikeOverkill end it the same way]], and is willing to blow up his own men to do it. His [[FreudianExcuse sole motivation]] is that he was [[EvilIsPetty bullied by Coordinators]] [[DisproportionateRetribution when he was a kid]]. ''Anime/MobileSuitGundamSEEDDestiny'''s sidestory, ''Anime/MobileSuitGundamSEEDCE73Stargazer'' adds some further atrocities to Azrael's name, showing that he regularly [[WouldHurtAChild took children from their parents]], put them through TrainingFromHell and [[BrainwashedAndCrazy brainwashed them]] with anti-Coordinator propaganda in an effort at creating pilots who could match Coordinators in combat, without the [[PsychoSerum drug problems]] of the Extended. Other villains might kill more people, but when it comes to the spreading of sheer human misery, no other villain in the ''CE'' verse can hold a candle to Azrael.
* DeaderThanDisco: Seed's success spawned a [[Anime/MobileSuitGundamSEEDDestiny sequel]] and a [[Manga/MobileSuitGundamSEEDAstray manga spinoff series]], and even started talks that the CE timeline could become the new UC. However, a planned movie to wrap up the saga is in DevelopmentHell, making creators and fans give up on the saga and move on to ''Anime/MobileSuitGundam00''. Today, if you ask Gundam fans of their opinion of Seed, you will get plenty of contrasting responses, and you certainly won’t find many fans of Destiny.
** Though the new HD remastered version of Seed that recently came out ''may'' have changed that.
* DieForOurShip: If you like Kira/Lacus, Flay is a rapist whore. If you like Kira/Flay, Lacus is a MarySue. ''There is NO middle ground''.
* DracoInLeatherPants:
** Muruta Azrael. Some fangirls either downplay or handwave his atrocities in the show because he's so pretty and hot.
** Shani, Clotho, and Orga get the same treatment. Yes they're SlaveMooks forced into the war by Azrael, but that doesn't make them any less [[SociopathicSoldier vicious]] or [[AxeCrazy insane]].
** Do we even need to bring up [[OmnicidalManiac Rau Le Creuset]] and the leather pants fangirls give him?
*** In the case of Rau and Azrael, people that hate the show also love them because they desired genocide and said haters are of the opinion that Cosmic Era is a horrible world that deserves for everyone in it to die.
* EnsembleDarkhorse: Although being TheFaceless, TheVoiceless, and a bigger SacrificialLamb than everyone else put in the series together, Rusty Mackenzie has a bigger fandom than you'd expect. [[AllThereInTheManual Supplementary materials]] have helped a lot, revealing him to be a friendly guy who was the only Redshirt of the Le Creuset team who didn't have a parent on the PLANT ruling council.
** Dearka Elsman. Between [[DeadpanSnarker his sense of humor]], his CharacterDevelopment, and [[BelligerentSexualTension his relationship with Miriallia]], he's quite well-liked.
*** [[AntiVillain Nicol]] and [[SociopathicSoldier Yzak]] arguably count as well (making all of Zala team besides Athrun an example of this trope), with the former liked for his NiceGuy tendencies and the latter for his [[HairTriggerTemper entertainingly vitriolic personality]] and banter with Dearka. That said, both characters have their detractors, particularly Yzak for his [[JerkAss Jerkassery]] and [[spoiler: destroying a civilian shuttle early in the show]].
* EvilIsCool: As the show's resident CharClone and MalevolentMaskedMan, everyone knew Le Creuset was going to be cool. Then the reveal comes in, and he turns out to be not only an AcePilot and a total {{Badass}}, but an impossible combination of Char, [[StarWars Emperor Palpatine]] and [[SilenceOfTheLambs Hannibal Lecter]]. Muruta Azrael also gets this treatment, both from fangirls who [[DracoInLeatherPants give him leather pants]], and others who find that his enthusiasm, [[LaughablyEvil dark sense of humour]], and status as a CompleteMonster with [[AttentionDeficitOohShiny ADHD]] make him a lot of fun to watch.
* EvilIsSexy: The fangirl opinion of Azrael. [[NauseaFuel Feel free to be ill]].
* FoeYay: Kira and Athrun of course getting this for being childhood friends turned into enemies. The FoeYay disappears in the second half though.
* HilariousInHindsight: Fllay hating the genetically-modified Coordinators. Her [[TabithaStGermain English voice actress]] goes on to voice the genetically engineered super-soldier [[Anime/MobileSuitGundam00 Soma Peries]].
** [[Creator/HiroYuki Clotho's Japanese voice actor]] dubbed [[WesternAnimation/SouthPark Stan Marsh]] for a while. Can you now say [[spoiler:[[TheyKilledKenny OH MY GOD! THEY KILLED CLOTHO!]]]] at the end of the series?
* ItsTheSameSoItSucks: This series is the AU series that is the most like the UC shows, due to the similarities between the Earth Alliance/ZAFT and Federation/Zeon conflicts, which might be a factor into why it's a frequent target from UC fans.
* LoveToHate: Rau Le Creuset, who is incredibly popular due to his [[MagnificentBastard brilliance]], [[{{Badass}} badassery]], and [[BreakingSpeech ability to give a speech]].
* MagnificentBastard: Rau Le Creuset fits this trope incredibly well. He does have a VillainousBreakdown but not much of one, goes out with a smile, and most importantly is a fine ManipulativeBastard and {{Chessmaster}}. When you [[spoiler:talk the world into self-destruction, manipulating a pair of ''very'' high-functioning {{Smug Snake}}s in the process, you count]].
** He's also clever enough to maintain his facade of wholesomeness until well after (in his mind at least) his plans have reached the stage where no logical reason remains to believe they can be thwarted. Rau Le Creuset isn't going mad during the final battle; he's having ''the time of his life''. [[spoiler:He even dies with the absolute belief that he is taking the whole of mankind with him - as evidenced by the almost seraphic smile on his face just before GENESIS obliterates the Providence.]]
* MemeticBadass: Arnold Neumann, the helmsman of the Archangel, thanks to his ImprobablePilotingSkills.
* MisBlamed: As mentioned many times on this page, many of SEED's detractors take Destiny's flaws and put them onto SEED instead of focusing on SEED's own flaws. In fact, even though there were a lot of changes in production just like Destiny, they improved the overall quality of the series. Not that the FanDumb will listen when you bring this up, of course.
* MoralEventHorizon:
** It's easy to lose respect for Rau Le Creuset [[spoiler: when he nonchalantly uses his [=DRAGOONs=] to kill Flay Alster, who had by this point redeemed herself.]]
** And then there's Patrick Zala [[spoiler: shooting Athrun]]. And pretty much everything Azrael does, most notably using PsychoSerum to turn kids into {{Super Soldier}}s, and using nuclear weapons as though they were going out of style. Captain Sutherland and the Earth Forces as a whole crossed it after the incident at JOSH-A with the Cyclops system.
** Depending on who you ask, some members of the fanbase feel that Yzak Joule crossed this when he [[spoiler:shot down that shuttle]]. Even taking what he thought was going on into account, he still believed he was firing on fleeing soldiers, a less than admirable act. This is possibly the reason why in ''VideoGame/SuperRobotWarsAlpha'' 3, that scene was modified and the civilian shuttle was shot down by random ZAFT pilots, rather than Yzak.
* NeverLiveItDown: If fandom is to be believed, then Kira's a bad pilot and Flay's an irredeemable bitch.
* NoYay: It isn't hard to interpret [[CompleteMonster Azrael]]'s interactions with [[SergeantRock Natarle Badgiruel]] as an attempt at hitting on her. {{Squick}}!
* OneSceneWonder: The [[AllYourPowersCombined Perfect Strike]] in the HD Remaster. Only appears in two episodes (the Battle for Orb) and is never seen again (despite being edited into the 5th opening).
* RootingForTheEmpire: Some fans ended up rooting for the Earth Alliance because of the insane disparity between the kill ratios between the Alliance and ZAFT. Especially since many sympathetic POV shots indicate that most of those poor Earth Alliance bastards getting killed are just doing their jobs at the behest of raging bigoted lunatics instead of being raging bigoted lunatics themselves.
** The fact that the EA soldiers and pilots are also all normal people while ZAFT is entirely made up by what the show directly states to be genetic engineered super humans further enhances this feeling. It also doesn't help that the first high-ranking Earth Alliance official we really get to know, [[ReasonableAuthorityFigure Admiral Halberton]], was a pretty cool guy who [[WouldNotShootACivilian shot down Natarle's suggestion that they conscript Kira into the military.]] He ended up dying tragically with his command, the 8th Fleet which was completely wiped out except for the ''Archangel.''
* TheScrappy: Flay Allster, [[BaseBreaker for those who don't see her as a]] JerkassWoobie. Her manipulation of Kira combined with her blaming him for her father's death, her racism, her bitchy personality, her treatment of Sai, and her general uselessness make her a pretty difficult person to like.
* TearJerker: [[TearJerker/MobileSuitGundamSeed Grab a pack of tissues and click this link.]]
* TheWoobie:
** IronWoobie: Go ahead life. Torture Kira. He'll get over it, eventually.
*** Athrun Zala can also be considered this. Lost his mother in a nuclear strike, has to fight his long lost best friend, [[spoiler: watches two of his closest friends and allies die]] due to his hesitation to fight Kira, has a [[spoiler:GeneralRipper]] for a father, and is too socially arkward to emote or channel any of this grief until it boils over the top and he breaks down. Yet, he still manages to be possibly the best pilot in the series.
*** If you're charitable to Lacus, she fits in like a hand to a glove. She's sheltered, ultra naive and kind of a PuritySue -- but when the chips come down, she does her best to gather her resolve and do what she can to help. Only once she breaks down, and that's when [[spoiler: she cries in Kira's arms while telling him about her dad's death.]]
** JerkassWoobie: Flay Allster, especially once she has her HeelRealization and tries to redeem herself. On one hand she's a self-absorbed, prejudiced and flawed FilleFatale who's hellbent on revenge and manipulates the hell out of Kira. On the other, she's also a desperate girl who pretty much lost ''everything'' and barely knows how to handle herself in the world until her CharacterDevelopment kicks in.
* TheyChangedItNowItSucks: The Remastered version is by and large the same, but there are small touch-ups and additions of scenes here and there. One notable instance is in episode 36 which adds a shot of [[CallForward Shinn and his family]] trying to flee the fighting. Probably the bigger change is in the ending themes: the first ending theme was remade and sounds somewhat different, while the original 2nd ending theme "River" by Tatsuya Ishii is omitted entirely and replaced with a new song by [[Music/YukiKajiura FictionJunction]]. Predictably, some fans of the original run have reacted much in the same vein as "Han shot first."
* TheyWastedAPerfectlyGoodPlot: An exchange between Siegel Clyne and Patrick Zala reveals that the Coordinators are a dying race. Due to genetic modification, later generations of Coordinators have a high risk of being sterile, which explain why [[ArrangedMarriage arranged marriages]] between fertile individuals are encouraged. The situation is so bad that it's actually a state secret. Clyne wants to reconcile with the Naturals to save their race while Zala refuse to do so, believing a cure could be found one day. This is never brought in the series again or in ''Gundam SEED Destiny''.
* ViewerGenderConfusion: Tons of viewers thought Nicol was a girl based on his looks, voice, and gentle mannerisms. If Youtube comments are any indication, he's STILL being mistaken for a girl over 10 years after the series aired in the Remastered episodes.
* JustForFun/XMeetsY:
** The beginning of the series looks like ''Anime/MobileSuitGundam'' meets ''Anime/MobileSuitGundamWing''.
** The setup for the final battle is '''Gundam Wing'' meets ''Anime/AfterWarGundamX'' with a little of ''[[Anime/MobileSuitGundam0083StardustMemory Stardust Memory]]'' added in.