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.
With both Harry being a Slytherin and Ron not meeting him on the train, Ron is set up as a major antagonist to Harry and his friends. Ron looks down on Slytherin, just as he does in canon. He's not evil (yet?) but he is a more extreme version of the canon character.
Hagrid is portrayed as an alcoholic rather than someone who has a drink occasionally. The author uses the same incidents of his drinking as are present in the canon, but they are viewed negatively by Harry's friends and thus by Harry.
Too Cool to Live: In Y2, Hermione, previously relegated to obscurity in Hufflepuff, once again attempts to brew Polyjuice Potion to infiltrate Slytherin. She is killed by the basilisk. The author has stated that he didn't have a subplot to deal with her and wanted to honor her by demonstrating her work ethic and determination (widely regarded as defining traits of Hufflepuff).
The only person of colour in Slytherin is written out of the story early on. (This is only a revision trope, and was due to the author not wanting to write an extra Slytherin into the story.)
Blaise is written back into the story as of Y5.
While it's probably made to make the audience cringe, Harry unfortunately has a case of Big Brother Worship for the misogynistic and borderline abusive Elan Malfoy.
The only female contestant in the Triwizard Tournament, the best her school had to offer, is defeated in a one-on-one duel by someone much younger than her. Which could be excused because it's Harry Potter; however, when Harry observes the male contestants duelling, he is overwhelmed by awe for their strength.
A quote from the chapter in question: "He couldn't out-duel her. That much was clear to him in the first few minutes. She was the best Beauxbatons had to offer. She had been trampled by a dragon and dragged into the depths of the lake by grindylows, but she was no slouch at her wand-work. Her movements were precise, her hands sure and steady. A steady stream of syllables rolled off her tongue, and the blasts of coloured light were giving Harry a steady workout to avoid. He couldn't keep this up forever. He couldn't cast as fast as her and dodging would only work until he made a mistake." Harry is clearly impressed with Fleur and has to resort to some unorthodox tactics. He causes her to slip and fall, breaking her wand arm. She then switches to using her other hand. "Harry was amazed at her tenacity. He hadn't realized she had such heart. That determined look in her eye was downright scary. Fleur wasn't as good with her left hand, and Harry got lucky as she miscast her shield and got hit with his Stunner. She crumpled to the ground. Harry, breathing heavy, didn't even have the wind to gloat."