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.
Americans Hate Tingle: Lacus is a Base Breaker bordering on The Scrappy 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.
In the HD Remaster, 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 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.
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 Suspension of Disbelief a little thin even though such role is preferred over an idol. She also comes off as a hopelessly naive Purity Sue who lucks her way into victory and power.
Kira himself. Some like Jesus Yamato and think it's excellent growth. Others find him a boring Canon Sue.
Deader Than Disco: Seed's success spawned a sequel and a 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 Development Hell, making creators and fans give up on the saga and move on to Gundam 00. 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.
Die for Our Ship: If you like Kira/Lacus, Flay is a rapist whore. If you like Kira/Flay, Lacus is a Mary Sue. There is NO middle ground.
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 Slave Mooks forced into the war by Azrael, but that doesn't make them any less vicious or insane.
Do we even need to bring up 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.
It's the Same, so It Sucks: 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.
Mis-blamed: 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 Fan Dumb will listen when you bring this up, of course.
It's easy to lose respect for Rau Le Creuset when he nonchalantly uses his DRAGOONs to kill Flay Alster, who had by this point redeemed herself.
And then there's Patrick Zala shooting Athrun. And pretty much everything Azrael does, most notably using Psycho Serum to turn kids into Super Soldiers, 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 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 Super Robot Wars Alpha 3, that scene was modified and the civilian shuttle was shot down by random ZAFT pilots, rather than Yzak.
Never Live It Down: If fandom is to be believed, then Kira's a bad pilot and Flay's an irredeemable bitch.
One-Scene Wonder: The 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).
Rooting for the Empire: 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, Admiral Halberton, was a pretty cool guy who 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.
Iron Woobie: 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, watches two of his closest friends and allies die due to his hesitation to fight Kira, has a General Ripper 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 Purity Sue — 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 she cries in Kira's arms while telling him about her dad's death.
Jerkass Woobie: Flay Allster, especially once she has her Heel Realization and tries to redeem herself. On one hand she's a self-absorbed, prejudiced and flawed Fille Fatale 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 Character Development kicks in.
They Changed It, Now It Sucks: 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 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 FictionJunction. Predictably, some fans of the original run have reacted much in the same vein as "Han shot first."
Viewer Gender Confusion: 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.