Americans Hate Tingle: Like SEED, Lacus is unpopular in the west even though she's one of the most popular characters in Japan.
Author's Saving Throw: The director's cut OVA is favored over the television series' finale for its new animation, the exploration of Durandal's character and the extended ending that expanded on the original that left viewers a really bad taste.
The four-part compilation movie 'Mobile Suit Gundam SEED Destiny: Special Edition' retelling the entire series from Athrun's perspective with some Revision. See the list of changes at The Other Wiki.
While not all of the changes could be retained for the HD Remaster, the latter does it's best to include as much of the material from the Special Editions as it can. This is mostly evident with music introduced in the Special Editions, but also about 90 percent of all of the animation from the Special Editions are used instead of the original broadcast, such as Kira and Shinn's first encounter.
The HD Remaster also got this when the Kira's fight scene in the Strike Rouge was completely remade to take advantage of the mobile suit's capabilities. As a common complaint regarding Kira is that he just "relies on Beam Spam to win", it further shows that, when he's in a weaker mobile suit, he is not completely invincible (the Strike Rouge is trashed in the fight, though he survives), and he can still fight in cool and surprising ways. It is considered the highlight of the HD Remaster.
Awesome Music: The debatable quality of the series does not extend to Toshihiko Sahashi's soundtrack, which is some of the best composed for anime with a seamless combination of orchestral, electronic, rock, and cloral numbers. The theme songs are no slouches either (with the arguable exception of the 4th opening). Whenever you hear T.M.Revolution singing you know that Kira (or Shinn in Special Edition) is going to do something amazing.
The 4th opening's actually remarkably good, it's just not a song for an opening. The real problem with the 4th opening (not to say it worked as an opening), was that the new ending theme and previous opening themes were still much stronger than it was, so "Wings of Words" never stood a chance. When the show was first airing, it was derided (at least among the English-speaking fandom) for sounding like it fit more in a romantic drama than in a mecha war series. It seems the Japanese producers agreed, as the HD Remaster replaces "Wings of Words" with "Vestige" by T.M.Revolution for the fourth opening.
Base-Breaking Character: Almost every character in the series gets this. This is how controversial the series is. Some highlights:
Broken Base: Possibly one of the most controversial Gundam series ever.
Ask in a forum who is the series' main character and you prepare for one of the longest discussions ever. People will keep repeating the names of Shinn, Athrun and Kira and rarely reach an agreement. It doesn't help that Athrun also happens to be the main narrator from the compilation movies and the one with the most screentime.
Athrun/Cagalli's relationship is a huge source of debate, due to the fact that no one seems to know what is going on with the two by the end. Were they really subjected to Ship Sinking or are they still together, just focusing on rebuilding Orb? The fact that fake interviews and rumors have muddied the water doesn't help this at all. That they are also always depicted together like the other two main couples in the series has also made it even more difficult to tell.
Catharsis Factor: For all the controversy surrounding all sides (except for the unambiguously evil and corrupt Earth Alliance), these is at least one moment of pure comeuppance given to both sides of the Archangel crew and ZAFT, particularly to their main pilot(s).
After sending many episodes abusing his Omniscient Morality License, even followers of the 'Church of Jesus Yamato' can agree that Kira's defeat at the hands of Shinn was a longtime coming.
On the ZAFT side, for those that have a hard time tolerating Shinn's wangsty behavior, seeing him on the receiving end of Athrun's (ineffective) Corporal Punishment can be very alleviating. Possibly the best moment for many was after the aforementioned battle where Shinn defeated the Freedom and supposedly killed Kira; Shinn, on absolute cloud nine, essentially brags to Athrun about his victory and that he avenged Athrun's defeat by Kira in an earlier battle. Infuriated that Shinn would actually think that he would be proud of him killing Kira, Athrun grabs him by the collar and throws his bravado back at him. It eventually accumulates to the point where Shinn asked Athrun if he would prefer that he had perished instead, causing Athrun to finally lose it and deck Shinn full in the face.
Complete Monster: Lord Djibril is Muruta Azrael's successor, with all of his predecessor's bigotry, but none of his intelligence or charisma. Having returned Blue Cosmos to its terrorist roots, he continues the Extended program; exploits the tragedy of the Junius 7 Colony Drop, opening the war with a nuclear assault on the colonies; unleashes the Destroy, piloted for one of his Extended, on Eurasia—leading to the deaths of thousands, if not millions, of civilians—personally kills over a million innocents with the superweapon Requiem while bragging about having the guts to do it; and is responsible for turning Mu La Flaga into his minion Neo Roanoke. Convinced that his own survival is paramount above all else, Djibril cowardly and regularly abandons his allies when the going gets tough and entertains plans of ruling the world when the war is over. A low-functioning sociopath with access to unlimited resources and technology, and determined to annihilate the Coordinators as a race, Djibril was a combination of impotent rage and cowardice, but with the money, influence, and total immorality to make him horrifying instead of merely pathetic.
Critic-Proof: Mobile Suit Gundam SEED Destiny is very popular among the Japanese audiences and even won the Anime Grand Prix award for Most Popular Anime in 2004 and 2005. Western reviewers liked the series but not as much as its prequel. However, if you ever ask this to a Gundam fan prepare to hear how this series is one of the worst things Sunrise ever created.
In a nationwide poll asking what readers of Gundam Ace thought was the best Gundam series, Gundam SEED Destiny ranked 12th out of 20 entries despite selling more than most entries that was ranked above it. Its Gunpla sales were also a huge disappointment for Bandai. While Destiny was popular with general audiences, most everyone was highly critical of it.
Critical Backlash: Over time, the show's hate has started to die down compared to more recent entries such as AGE and Reconguista in G, with the general consensus being that while it does have some glaring flaws, it's not as bad as its haters say.
Designated Hero: The Three Ships Alliance never seem to get called out for their own errors and come off as Karma Houdini. This includes their "rescue" of Cagalli that sparked a disastrous offensive by her incompetent groom and their "intervention" in PLANT's invasion of ORB to arrest LOGOS members, which indirectly led to a few of the colonies being blown up thanks to Djibril's escape.
Die for Our Ship: It's hard to know which girl of the Athrun Harem takes more bashing from fans of the other girls, though Meer and Meyrin get it particularly hard. Not even Cagalli was safe.
Yzak and Dearka too, to the point where fans wanted them to have a bigger role in the story.
Fanon Discontinuity: Many fans who feel that SEED didn't need a continuation or just don't like the characterizations of its returning cast or the writing prefer to pretend that this series never happened.
Fan-Preferred Couple: This show sankboth Dearka/Miriallia and Athrun/Cagalli. Considering that both of those pairings were quite popular among the fandom during the first show's run, the reaction was predictable. The fandom's solution is to have them make up after the series ending and get back together again, if fanfic is any indication.
Although she was present in Gundam SEED, the fact that Shiho appeared more frequently in this show upped her popularity and really kick-started the Yzak/Shiho fanbase. Prior to this, fans of Yzak looking to pair him with someone tended to do so with either Dearka, Flay (simply due to the fact that she was the only major female character he was around late in the series), or even Cagalli. Once people started noticing Shiho, she quickly became the favorite for Yzak, and the other pairings were largely forgotten.
Germans Love David Hasselhoff: Despite being hopelessly irrelevant, the Blast Impulse is very popular with western fans for its unique color scheme and payload. It's almost completely ignored by Bandai, with an 11-year gap between its Master Grade kit and the MGs for the Impulse's other non-MSV forms and it did not have a High Grade kit until almost 11 years after the final episode aired.
In episode 23, the insert "Meteor" by T.M.Revolution plays before the death of a character voiced by T.M. The fact that the theme ended just before the character was killed made people wonder if he decided to sing before being killed.
Gilbert and his speech about his Destiny plan is humorous when you realize Wufei made statements about "getting rid of all evil" (both characters are voiced by Ted Cole). And in the Endless Waltz, Wufei was even willing to become evil to achieve peace.
Sting's "I'm practically non-existent to you, am I?" quote (coincidentally) foreshadows a long-running meta joke (the men's existence) in the Love Live! franchise.
In the battle between the Earth Alliance Orb fleet and the Minerva, the Archangel and Freedom barge in and attack both sides. Combine Kira's disabling tactics and the overall intention of stopping the battle in mind, this wouldn't be out of place of Season 1 Celestial Being's armed interventions.
It's the Same, Now It Sucks!: Some detractors of the series feel that SEED Destiny retreads too many plot points and character roles from SEED, with the finale (where the old cast takes over again) being a particular sticking point. Outside of that, the mobile suit designs ramp up the Universal Century cues to the point where there are actual Zakus as opposed to Zaku expies (like the GINN from the previous series).
Shinn's an unpleasant little jerk a lot of the time, but that doesn't make what he went through any less horrific. Many viewers want to hug him and slap him at the same time, screaming at him "YOU IDIOT! STOP RUINING YOUR LIFE AND OTHERS'!".
Auel and Sting seem to count for some fans, as they're massve jerks but are also mere pawns in this "game" of war and, as members of the Extended group, are deeply fucked up in all senses.
Magnificent Bastard: ZAFT Chairman Gilbert Durandal sees himself as the saviour of Earth and nearly persuaded most of the planet to go along with it. Presenting himself as a moderate and a pacifist, Durandal made use of Lord Djibril and Blue Cosmos' blatant evil to launch an invasion of the Earth Sphere disguised as a liberation, using his own reputation for honesty and the services of Lacus Clyne impersonator Meer Campbell to camouflage his intentions, and scattering agents of FAITH throughout the ZAFT military to keep an eye on its loyalty. Preying on the emotional insecurities of those in his service, Durandal turned Decoy Protagonist Shinn Auska into the very thing he hated most and kept veteran characters like Kira, Athrun, and Lacus out of the picture or unsure if they should oppose him for most of the series. Only killed when he loses the faith of his most loyal enforcer, Rey, Durandal dies convinced that he was right and that without his Destiny Plan, the world is doomed.
Destiny itself is considered a huge case. Years since the end of the series, and even after its more popular handling in the Super Robot Wars games, haters will never get over their hate towards the series and its characters.
During one of her first sorties with the Impulse, Luna has an opportunity to destroy a shuttle carrying a fleeing Djibril into space. She misses and he escapes. This one thing has eternally defined her character for some people, though it was already established in episode 7 that Luna was a lousy shot during her target practice sessions. (Which makes it more Talia's fault for assigning the long range bombardment weapons to the worst shot of the trio.)
Athrun's role got some criticism to the point of being listed as the dumbest Gundam character in an official Sunrise poll. No matter that it stemmed from mental issues (like Conflicted Loyalty which Durandal exploited) and he returned to his normal level of competence once he got over them toward the end of the series.
People often like bringing up Shinn whining about his parents and sister when in the show he stopped doing it openly pretty quickly.
Replacement Scrappy: Shinn, who seems to have been an attempt at creating a darker, more conflicted Kira. It didn't work. It should be noted that Shinn was the third most popular male character in the CE franchise (behind Kira and Athrun), based on the then-current NewType and Gundam Ace character polls.
Ron the Death Eater: Fans who disagree with Kira and Lacus' tactics often forget their motives and try to turn Kira into Rau 2.0. The actual Rau 2.0, Rey, also suffers from this at the hands of fans who Flanderise him into an irredeemable bastard, while forgetting his admiration for Durandal, good intentions, and what may have been a genuine friendship with Shinn. Which ironically demonstrates the flaws in the Destiny Plan that Rey believed in so much; he was genetically identical to Rau yet a distinctly different person.
Rooting for the Empire: The numbers of those who were already rooting for the Earth Alliance in the previous series (since it had some sympathetic POV shots) swelled when they practically became Card Carrying Villains in this one. It did not help that some of the portrayals came off as political Take Thats. The people who root for ZAFT, conversely, tend to fall under Draco in Leather Pants.
Scapegoat Creator: The level of hatred that the most rabid anti-fans deliver towards Fukuda and Morosawa sometimes reaches disturbing levels. It doesn't help that they have a reputation as Lying Creators that may be entirely due to poor fan translations of the relevant interviews, plus a supposed "Morosawa interview" that was apparently fully made up by haters.
The Scrappy: The Broken Base may fight over just about every aspect of Destiny, but just about nobody on either side likes the DOM Trooper pilots. Poor characterization plus overuse of Zeon Expies equals Black Tri-Stars clones who spout lines like "You'd have to be pretty messed up to disagree with Lacus-sama!" Shinn fans hate them for being one-dimensional zealots, while Kira fans hate them for Not Helping Their Case. Even many Kira fans were left wishing that that Shinn or Luna would subject the DOM pilots to the Black Tri-Stars treatment, especially since that would've made the finale seem like less of an unrealistic Curb-Stomp Battle and more like something Kira's side had to actually work for.
Signature Scene: The battle between the Freedom and Impulse. Even many who despise the series praise this fight, and a lot of the Impulse's later model kits and figures include accessories to be able to recreate the finishing blow.
Shocking Swerve: Mu La Flaga's survival makes no sense, even in a series that uses the Unexplained Recovery trope frequently, as there was no ambiguity about his presumed death since his helmet was seen floating in space among his mobile suit's wreckage. The Special Edition and HD Remaster both perform an Orwellian Retcon to try to remedy this.
Strangled by the Red String: Shinn's and Lunamaria's respective first loves are Stella and Athrun. Stella dies tragically, Athrun, along with Lunamaria's sister, Meyrin, defect, are shot down by Shinn and presumed to be dead. They got better. Lunamaria and Shinn end up together but due to the way it was handled, they are widely believed to have been this. The Special Edition is a little better about this.
They Changed It, Now It Sucks!: While there aren't too many complaints about replacing "Wings of Words" with "Vestige" as the fourth opening theme, all of the instances where the latter was used as an insert song being cut out has been less well-received. The Strike Freedom's first launch in particular loses much of its impact due to Vestige being replaced with instrumental music.
Basically nothing about Neo Roanoke's identity is played to its full potential; most of the implications (such as the parallels between his situation and the Destiny Plan) are never even addressed, let alone things the fanbase was made to expect, like an armed conflict between Phantom Pain and the Archangel. Nor did they bother to have him become The Atoner for the horrible things he did while brainwashed, instead just having him go straight back to being SEED-era Mu La Flaga as if regaining his old memories caused him to forget all about being Neo.
The halfway mark of the series has the Minerva crew discover the lab where the Extended were created, and see the records of exactly what horrible things Lord Djibril did to make them. It's treated like a big important moment in the story...that never comes up again.
Tough Act to Follow: Even though it was still a ratings success, it was preceded by the show that had the second highest ratings in the franchise. There was no way it was going to keep up that momentum, which resulted in the perspective flip as well, to try and up the ratings.
Neo Roanoke was supposed to be a Tragic Villain who regretted his actions but thought he had no choice, like breaking his promise to Shinn to never let Stella enter the battlefield, which was later implied due to him being brainwashed. But that moment painted him as a Jerk with a Heart of Jerk witch undermined his prior redeeming traits, and it's ambiguous how much of his actions were due to brainwashing. He HeelFace Turn upon realizing he was brainwashed was supposed to redeem him, but he did so for reasons other than his prior actions, never got to anything related to atoning (like fight his former masters), and shows no regret and suffers no consequence for his past deeds once he does. Super Robot Wars Z fixes this by having him express open regret for his actions after defecting.
Vindicated by History: Many will outright praise its handling in Super Robot Wars Z which means that Destiny had lots of good ideas and concepts, it was just how they were executed that pissed a lot of Gundam fans off .
While the series itself is still controversial, it has mostly been given a re-evaluation thanks to both Super Robot Wars and the introduction of Mobile Suit Gundam AGE, the latter of which is widely regarded as far worse.