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.
Anticlimax: The last few chapters build up to a deluded Dumbledore preparing to attack and kill Harry. Then Dumbledore ends up battling a vision of Harry in the Room of Requirement, never gets near the real one, and is captured effortlessly afterwards. It's not a surprise given how they seem to breeze through all obstacles in the new timeline, which makes the way they were so comprehensively defeated in the old timeline look even more out of place.
I'm guessing that later in the story, Harry will be framed and sent to Azkaban, allowing his hitherto unknown twin who's the actual Boy Who Lived to take his place, get adopted by Snape and become Head Boy, upon which he hooks up with Hermione (who turns out to be really a pureblood) at the annual Yule Ball and they have lots of rampant sex in the Head Boy and Girl's private quarters, and meanwhile Draco discovers that he's part-Veela and hooks up with an American exchange student who's a newly discovered species of super-witch with an anachronistic taste in clothes and music, and they go off and fight the resurrected Salazar Slytherin together.note None of this actually does happen, but it wouldn't have been a surprise.
Designated Hero: Harry, arguably. In the new timeline, he destroys the Weasleys' lives for things they haven't actually done yet (including feeding Percy to Fluffy and rendering Ron sterile and unable to perform magic) and sees nothing wrong with doing so. Hermione, at least, does show a little angst and remorse.
Disproportionate Retribution: While Ron's sudden seizing of a Villain Ball and raping Hermione is, indeed, despicable, what Harry and Hermione do to Ron and the entire Weasley family in the new timeline is by far more amoral. First, Harry gets Molly arrested at King's Cross for trying to help him find Platform 9 3/4, proceeds to attack her and her family when she walks into the Great Hall (because he assumed she was going to attack him despite being unarmed), and then, to ice the cake, proceeds to force the entire Weasley family into destitution by suing them for damages. This despite the fact that, in this fanfic's canon, Harry is the scion of House Potter (being an "Ancient, Noble House of Potter fic, classism is inevitable) and being worth more than the entire family hundreds of times over in canon. As a result of Harry's actions, Arthur and Bill lose their jobs (because, for some reason, the goblins of Gringotts Bank now care about wizarding politics despite being disinterested and aloof in canon) and the whole family (sans Charlie) is homeless due to Harry seizing the house so he can tear it down and put up a generic McMansion.
Fridge Logic: So why would Voldemort protect parts of his soul with items that can be destroyed for a nominal fee?
The rationale for Kingsley not becoming Minister for Magic was that the Minister had to be a pure-blood. Then Pottermore revealed that the Shacklebolts were indeed an old pure-blood family.
Informed Wrongness: Snape is if anything more sensible and reasonable than he is in canon, which doesn't stop the story going on about how terrible he is.
As far as Ron and Percy in the new timeline are concerned, Harry and Hermione are a pair of stuck-up bullies who've got it in for them and their family for no apparent reason, yet we're supposed to think they're terrible people for resenting this.
Ron the Death Eater: Apparently, he's worse than the actual Death Eaters. Despite being a "shit wizard". So are the other Weasleys (except Ginny, strangely enough) and Dumbledore (though he at least is portrayed as merely paranoid, not completely evil).
Strawman Has a Point: Any time someone (usually Molly or Snape) goes off on one about how terrible Harry and Hermione are in the new timeline.
Unfortunate Implications: Despite being a "shit wizard", Ron is able to overpower Hermione, who's powerful enough to destroy the Dementor as it feeds on her, for what seems to be no other reason than that he's a boy and she's a girl. Also, becoming a girl (which a sufficiently powerful Groin Attack can do, an Unfortunate Implication in its own right) means that he won't become a rapist because apparently female rapistsdon't exist.
There's also the fact that for all the talk about her being a smart and strong witch, Hermione defers to Harry on most things, and whenever she starts questioning the morality of what they're doing, Harry is quickly able to talk her round to his way of thinking.
Honestly, Hermione's entire character arc in the first chapter is made of nothing butUnfortunate Implications. Let's start with the fact that Harry is a ridiculously overpowered Gary Stu, whereas she needs rescuing from a "shit wizard" who can't even hex a pair of Muggles successfully. Then consider that everything that happens to her serves only as a motivation for Harry's actions. That she shouts defiance at the Dementor in her final moments is very much too little too late.
Treatment of Hermione aside, the story is rift with the theme of women being overly emotional and needing to be restrained by their husbands. One scene has Hermione and Mrs. nearly attacking Mrs. Weasley, only to be restrained by Harry and Mr. Granger respectively, while Mrs. Weasley has to be forcibly restrained with magic, making her quietly sit in a chair, by Mr. Weasley. That Mr. Weasley resorts to using magic to overpower and silence his wife is shown as proof that he's "good" in the new timeline, and his canon behavior is described as him being "led by the nose", implicitly making him worthy of being mocked. The one reference to the women's behavior being good is Mr. Granger randomly thinking how much he likes Mrs. Granger's fiery attitude, in other words expressing it favorably by making it sexually enjoyable for a man. Um...
The classism. The Weasleys are poor and generally miserable, and only are shown mercy when they kiss up to Harry and Hermione, who are prominently referred to as "Lord and Lady Potter". This leads to Harry talking about how "merciful" he is to them, particularly in buying the Burrow and tearing it all down to replace it with a "superior" mansion.
Kingsley doesn't become the Minister for Magic because you apparently have to be British. This may have been a clumsy attempt to add racism to the ITWATN-verse's litany of sins, as though they needed to be any worse, but comes across as suggesting that black people can't be British. Oops.
What an Idiot: Several examples, but probably the worst is Harry putting hundreds of people's lives at risk by boarding a passenger jet in the full knowledge that he's at risk of uncontrolled magic. Don't wizards have their own methods of long-distance travel, anyway?