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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.
Broken Base: The anime producers overlapping the E-Pandora arc with the Bridget-sibling arc for the second season adaptation. Viewers are split amongst those who think it was a good idea, or not, to go this route.
Elizabeth Mably is considered one nowadays which says a lot given her rough introduction for being portrayed as nothing but a bully towards Satellizer. However, Elizabeth gained a lot of respect amongst readers due to her Character Development throughout the E-Pandora arc. It is here that she showed a much kinder and understandable side, particularly to the E-Pandora test subjects, which made her stand-off to Chiffon all the more satisfying due to the later going in the exact opposite direction in likability at this point in the story (See Alternate Character Interpretation).
Her Limiter, Andre Francoise, isn't too shabby either amongst fans. Shown to be perhaps one of the few capable Freezing supporters during the Pandora duel against Charles to the point that many wish for Kazuya to follow his example.
Game Breaker: The Aoi siblings, both of them. Normally a Pandora is supposed to be only capable of holding up to six Stigmata at a time – Kazuha had twenty. Kazuya's body is explicitly stated to be over 30% Stigmata tissue, such that he doesn't even need to partner with a Pandora to use Freezing. However, Kazuya only displays Freezing without a partner when he's sufficientlyenraged, and Kazuha... well, if you paid close attention to the backstories, you know what happened to her.
Informed Wrongness: Dr. Scarlett O'Hara gets chewed out and slapped by her superior, Dr. Aoi, for trying to advance their understanding of how the stigmata works, and how to grant Pandora abilities to those not innately born with the talent for accepting the stigmata. The only reason Dr. Aoi gives is that doing so would be 'tampering in the realm of God' and that they should be satisfied with what they've been given. Of course, it does go horribly wrong later on, but only because the higher-ups are desperate for results, and push Dr. O'Hara and her test subjects much faster than she wanted to go.
And as an added bonus, he has a project of his own that is essentially the same- Valkyrie
It becomes less "Informed" with The Reveal that the E-Pandora project was never anything but a publicity stunt to buy time for the Type Maria project.
And there's Chiffon Fairchild and Ticy Phenyl in Freezing: First Chronicle. Hell, When Chiffon dies, she has a huge goodbye with Ticy (in which Ticy fondly remembers being groped), while Chiffon's limiter (and in this series, Pandoras and Limiters are almost always closer to each other than to anybody else) is ignored.
We get more from Roxanne (not surprising) and Charles Bonaparte (very surprising). Charles appears to be closer to Rox than to her own limiter (remember what we just said about Pandoras and their Limiters) and is ridiculously tsundere towards her. Roxanne tends to look out for Charles and enjoyed giving her Marshmallow Hell. And later, Charles plants her own face between a naked Roxanne's breasts.◊ It's still there five pages later,◊ as well as eight pages later.◊ Neither of them seems to mind much.
Chapter 136 only adds to this. Charles' reaction to the possible death of Roxanne is similar to the reaction one would expect from someone who was about to lose a lover, and it's made clear that her friendship with Roxanne is more important to her than anything. The thought of losing Roxanne was enough for Charles to swallow her massive pride and beg Lana to find a way to save her, and her despaired screams were enough to help Roxanne pull herself back from her Nova Possession on Heroic Willpower alone, something nobody else has ever been able to do. When Roxanne kills herself to keep herself from fighting her comrades, her last words are for Charles, and after Roxanne dies, Charles crosses right over the Despair Event Horizon and keeps going. Until Windy May heals her and Charles Accelglomps her.
Louis is universally reviled by the fanbase because of his misogyny and inhuman treatment of both Satellizer and Holly.
Kazuya, despite being the protagonist, is seen as a scrappy to many due to always being seen as a useless protagonist throughout the story; the worst of it occurring in the Bridget-sibling arc.
Ganessa's Establishing Character Moment in the first episode sets her up to be an interesting character. Then she spends the entire second episode revealing herself to be the most punchable character in any anime ever. She starts a fight with Satellizer and forces her to fight back, claims not to care about her victory (which happened offscreen) but decides to brag about it anyway, and still has the nerve to consider her the one that needs to be taught a lesson. And all with one of the biggest Smug Snake attitudes to date.
She was Rescued, however, when she didn't hesitate to take the bullet for Satellizer, resulting in horrifying wounds.
Now we have Charles. So she was a bit of a bitch during the E-Pandora arc, but hey, she was just doing her job as a loyal soldier and daughter. During the Valkyrie arc... not so much. She callously insulted Elizabeth in front of the latter's friends, and when Attia demanded she apologize, she got curb-stomped and at least one of her breasts cut off by Charles out of spite. Needless to say, this didn't win her any fans.
Second Season Downfall: The second anime season, Vibration, was not as well-received as the first season due to how the producers went about adapting the manga materialnote Skipping ahead to adapt the Alaska arc, and then discovering that in the middle of the arc, they shoehorned the skipped Bali arc into a few episodes WITHIN the Alaska arc, and because the main cast remained mostly Out of Focus in favor of Character Development for side-characters such as Elizabeth, and the E-Pandora test subjects, that people were less invested in. To be fair though, the latter problem persisted in the manga as well.
Shocking Swerve: Louis' survival at the end of his arc. As is the backstory for Mark Spencer in Chapter 75.
The anime tones down Louis' actions, and seems to be aware of how poorly his survival was received in the manga. Instead of an attempted murder-suicide, Louis comes to realize just how horrible he is and throws himself from the cliff. Holly's attempt to die with him provides an element of Love Redeems, as his first thought upon waking up is her safety. It still seems like he got off easy, to many fans.
They Changed It, Now It Sucks: The 2nd anime season had this reaction at first for what looked to be the anime producers skipping over the Bridget-sibling arc to adapt the E-Pandora arc; with critics saying that by doing it, it would miss out on much needed Character Development for Satellizer. However, part way into the season, it turns out that the producers decided to overlap the Bridget-sibling arc with the following E-Pandora arc which calmed some of the earlier backlash and now creates a Broken Base amongst viewers (See Above).
Iron Woobie: Satellizer and Cathy, but the entire E-Pandora team deserves special mention. One signed on to the project to avoid starving to death and one was sold by her parents. The rest of them are implied to have even worse pasts.