Anti-Climax: 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 and Umbridge's mother was a Muggle.
Good luck re-reading the bit about the "secret ritual" for transferring the Horcrux into a pig and not thinking of piggate.
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.
Misaimed Fandom: The message of the books that you should not judge the person by who they were born apparently flew over authour's head considering how much Harry boasts about being from "Ancient and Noble House of Potter"
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.
Unintentionally Unsympathetic: The reason the original timeline was so bad was apparently because Harry and Hermione went off to Australia and left Britain to rot, and once they're back in time, they mercilessly bully the people who would have hurt them in the original future despite said harm having not having been done yet, and act like smug little twits about it all. The Weasleys (who this fic is about bashing), on the other hand, are Unintentionally Sympathetic.
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?