Alternate Character Interpretation: A lot of the controversy revolves around a reinterpretation of Katara and of the contrast between her Sugar Queen persona and the dark side she sometimes shows in canon. Some readers think its brilliant. Some see it as character bashing as well as a case of Ron the Death Eater. Some think they see where the author was trying go with this, but also think it was taken too far or otherwise poorly executed.
Arguments over the history and backstory of the Fire Nation and Vathara's world in general can also be volatile and comes down to four points of contention:
When it comes to the causes of the war, some people see "but"s that make the Fire Nation "Innocent" and others see "why"s that don't.
With loyalty, some see it as a gun to the head forcing the Fire Nation to do things they don't want to, making them victims and ultimately innocent while others see it as, at worst, a gun to the head of a gangster; sure, the gang will kill him if he tries to leave or go straight, but he joined up willingly and likes hurting people, so it's a non-issue.
Vathara's culture for the Air Nomads: did she make them evil baby stealers as part of a Humiliation Conga who deserved to die, or is it a valid interpretation of what's presented in canon?
The Gambit Pileup; some see it as part of a complex web of reasons, others see it as an excuse for the Fire Nation to go to war with the Air Nomads.
Crazy Awesome: Played straight with references to Bumi: 'we all need to think like mad geniuses.' Deconstructed with Zuko. Many of the things he does, like suggesting that people of fire and earth live together, escaping by amphibious train, using firebending and oil as a drill to free the Suzuran, following turtle seals under the ice and so on are regarded as absolutely insane. And yet he pulls them off. However, from Zuko's POV, these things are shown not to be acts of mad genius, but acts of desperation, very thoroughly planned out, and/or very possible given Avatarverse laws of physics. Not to mention several decades of experience experimenting with lost or novel forms of bending: Zuko didn't come up with most of that stuff, Kuzon did.
Iron Woobie: Zuko as well as his great-grandfather, Kuzon.
Koh seems to be spearheading the faction trying to wipe out humanity. Also, what happened during the attack on the Northern Water Tribe: killing the last healers and causing the public to lose confidence in him. And giving spirits carte blanche to kill lots and lots of people, mainly Aang's potential allies.
Wan Shin Tong appears to have a standing policy of having his agents steal records, even letters, from libraries containing any helpful information that might allow people to put two and two together.
Sozin using a hurricane to convince his people the current Avatar was out to finish what Kyoshi started and the only way to prevent it from happening again was to eliminate the knowledge of airbending.)
Yue taking command of the effort to preserve humanity, reviving the yaoren using Zuko as a test case, which, by the way, takes him out of the Fire Nation line of succession and basically means her people's enemies are screwed unless Aang restores balance.
Kuruk might have made a certain sexist statement in order to save the Water Tribes. It's notable that the healing benders of each element were wiped out during the term of their own avatar, with the exception of his. Koh might have gone after his wife because Kuruk was too good at his job, not because he wasn't doing it.
Kuzon forming a friendship with the Avatar in the first place, when his clan was sheltering renegade airbenders, might have been an attempt to cause Aang to reform the Air Temples. Then he turned Byakko into a refuge for dragons and enemies of the Fire Lord and spent the rest of his life Walking the Earth, making contacts and searching for Aang, with the Fire Lord's blessing since he thought Kuzon was spying on his behalf. Of course, Azulon eventually figured out he was being fed disinformation and had Kuzon killed. Alternatively, Shidan mentions that his family has been looking after Byakko for dragon-generations, so it's unknown how much of this was his plan. At the very least, he continued it after Kuzon's death and was the one to send Ursa to Ozai - and he seems quite proud that she killed Azulon.
Azula using Ty Lee's chi-blocking to prevent Zuko benefiting from practicing his kata and train fully, allowing Mai to end up in a Kissing Cousins relationship with him in order to blackmail them later, on top of canon.
Ty Lee is keeping secrets from Azula, which is stated to be very, very hard to do. An Air Nomad (or at least the descendant of one), making friends with the favored heir? Not to mention that in chapters 33 and 34, she uncovers plots as easily as Azula, hijacks them for her own purposes, is the only reason they're able to pull it off and gets Amaya to heal Azula. And she'll probably get away without Azula killing her for it, too. Averted partially in Chapter 35: she does get away with it, but it turns out that Azula has already known about her Air Nomad heritage for years now. She just doesn't consider them a threat, since airbending itself has already been wiped out.
Pakku for what he did to Katara's waterbending.
Misaimed Fandom: Can occur when the audience misses the intended subtext, or if the storyteller failed to make their point in a convincing manner. Devoted fans of the story tend to see critics as the first case, failing to understand the motivations Vathara has created for various characters, despite the extensive author notes provided. Critics see this as the second case, claiming that the story and notes fail to reconcile the characters behavior with character development seen in dozens of canon episodes that are unchanged in this alternative timeline. Several paragraphs of debate on this and related subjects have been moved to the discussion page.
Moral Event Horizon: General Fong goes flying over it in Chapter 70 when he forces civilians to walk straight into Dragon's Wings' trapline after Zuko's forces/traps kill most of his scouts.
Ron the Death Eater: Katara's season three rage over Zuko getting Aang mostly-killed after she'd started to trust him is transposed into a season one homicidal fury that Zuko is of the Fire Nation and has the nerve to be a better healer than she is. Since then, Katara has been publicly humiliated by Zuko in three or four different ways and has been reclaimed as an acceptable being, but is being used as a prop in the new goal of showing that Aang is a horrible, selfish boy who is deeply intolerant of everything that doesn't fit into his childhood culture (which, by the way, is secretly evil).
The Scrappy: For a number of readers who don't buy into the alternative character interpretation, Katara becomes this at some point in the chapters before or after the end of the Ba Sing Se arc.
The Fire Nation's justice system is utterly alien; The Water Tribes, Air Nomads and Earth Kingdoms have familiar ethics-based legal systems (assumption of innocence, punishment of the guilty, reparation to the injured) enforced by the heads of their communities. Competence and integrity may vary, and they may disagree on minutiae, but they can comprehend each other easily enough. The Fire Nation has a sociopathically selfish approach to justice: the only reason not to commit a hostile act is if the person you're attacking will kill you for it, and if they don't have the ability to stop you, then they deserve to lose property, to suffer pain and to die unlamented - Might Makes Right. The other nations dub this "homicidal mania."
Shidan:...to not take up weapons, to not prepare night and day to slaughter any enemies that would come against them - it is unthinkable. It is - one who does such a thing, who believes the world will not be dangerous, will not strive to kill him... That is what we call insane. ...And it is our dangerousness, our peril to each other, that keeps each clan from another's throats. If one member of the clan will not fight, and other clans know that to be true...
Langxue: They stomp on him, everybody else comes roaring in to fight, and the whole countryside goes up in flames.
This even applies to warfare. Zuko believes the War is wrong because the Fire Nation will be unable to hold its new territories, and as a result be unable to prevent retaliation by the other nations - retaliation that will kill pretty much everyone in the Fire Nation. He doesn't believe that the war is immoral, just unsuccessful. Vathara suggests this is inherent to their culture - a throwback to the constant state of clan warfare in which the only law was; "War is only immoral if you lose."
Zuko: I wish I could stop the war, Toph. I really wish I could. But I can't. Because you know what will happen if it stops? They'll come for us. The Earth Kingdom, the Water Tribes you have no idea how much they hate us. They'll come.
The Air Nomads have faith in freedom to the point that Aang doesn't understand that people can and will do things they don't want to do, let alone that people can make others want what others want. His belief in the sanctity of life is downright insane to the hunter instincts of fire and the hunter survival needs of water. The concept of true evil that one can not reason with is totally outside his worldview, and the pacifism of his culture is called into question as there are more definitions of harm than physical injury.
The Water Tribes' orientation towards community often means that "good" is what benefits people inside the community of the tribes. Any crime against a member of the tribes from an outsider is 10 times worse than the same crime going the other direction. Members of the tribe who do evil are the tribe's responsibility. An outsider striking down an evildoer of the tribe is still attacking the tribe, even if the tribe would do much the same to the evildoer if they had the chance to do so.
The Woobie: As of Chapter 31, Katara. Her tribe hates her and her own father threatens to kill her for something she wasn't aware she was doing. On top of that, Aang says she's a horrible person and reveals that there's no way they can ever be together unless Katara's willing to abandon her children the Airbender way; the way she lost her parents by her mother's death and her father's abandonment of the family... Toph is outright horrified by how Katara's treated, and Zuko feels as though doing this might have been horrible enough to mean he shouldn't be allowed to rule anyone, and feels compelled to write an apology even though he's from a culture based on cultures where apologies are considered worse than useless, what matters is actually taking action. Which he does, by sending her a way to both avenge her mother and get away from the people who have shown her they don't love her.
What an Idiot!: During his spirit-encounter with Roku, Zuko all but calls Roku an idiot for failing to see he could have prevented the war by undoing the unnatural situation Kyoshi had put them in, as well as for failing to accept his guilt in the matter. In Roku's defense, it's heavily implied that as a Fire Nation Avatar is born devoid of Loyalty, the suffering the Fire Nation was undergoing after having been forced to adopt a more Earth Kingdom-like social structure just passed over Roku's head. Roku himself doesn't even seem to know (or at least understand) that Loyalty, in a Fire National, is literally the difference between life and death.