There is the fact that in my mind Harry never really accomplishes anything by himself apart from the patronus in book 3. Hermione/ron/mother’s protection walk him through the challenges in 1st year. Second year is Fawkes/sorting hat and a whole lot of luck. 3rd year Hermione with the time turner sets up the climax (although again Harry’s patronus is all him). 4th year he is guided through tournament by moody/crouch jr. 5th year he is an angsty teen who falls for an obvious trap (ignoring the mirror he has to call Sirius and relying on Snape of all people), and is saved by Dumbledore. 6th year he is an angsty teen who doesn’t stop Draco, doesn’t stop snape, doesn’t do anything and the one thing he is good at (potions) is a result of Snape’s old book. 7th year he wins because of some bs deus ex machina with the Deathly Hallows. Very little of what he actually accomplishes is due to him. In fact, I think canon Harry is pretty blah. It could be argued its due to the abuse, but he is a mediocre student who takes easy classes over arguably more useful ones, and turns into a giant angst ball his 5th and 6th year.
I dislike the fact that Dumbledore is either incompetent, or possibly malicious. At the very least his motives must be suspect. How does a possessed Quirrel teach for a year with Dumbledore not knowing? How does he even get by the wards? How can Hermione, a 13 year old first generation witch, although a very smart one at that, figure out the monster in chamber of secrets when nobody else can including a 100+ year old Dumbledore. Speaking of that, he knows that Hagrid is innocent, but doesn’t push for exoneration on his behalf despite being the head of the Wizarding court. In that same vein, he knows Sirius is innocent, but instead of doing something about it himself sends Harry and Hermione back in time on a very dangerous mission to free him. Then once he is free never pushes for a trial or exoneration of any sort despite being one of the most powerful (politically/magically) wizards in the world as we are led to believe. His supposedly good friend and comrade Mad-Eye Moody is impersonated for an entire year by a polyjuiced crouch jr (again wards hello?) and kidnaps Harry right in front of him. Dumbledore’s only defense around the goblet of fire was an age line, which was just asking for problems. Also, do you mean to tell me that someone could have put a first-year in the cup and had it draw them and people would just shrug their shoulders and said they had to compete? please, even in the nonsense world of magic contracts would have to be knowingly entered or the potential for abuse is far to great (take this hilarious fanfiction for example). 5th year umbridge takes over the school and gets away with torture. Dumbledore does nothing. 6th year he allows Draco to basically plot his death, almost killing another student in the process and allowing death eaters in at the end of the year. Even after he’s dead he basically screws with everyone. A children’s story book, a snitch with a riddle, and a trinket? wow… Then he tells harry to off himself which is great.
If you take the view that Dumbledore is a good guy, then he is very, very incompetent (or senile). If he isn’t incompetent, as someone who is head of three incredibly important positions should not be, then he is certainly not a good guy, potentially even malicious as the common fan theory suggests.
Also, and this is just personal preference, I hate the Harry/Ginny pairing and I hate the Ron/Hermione pairing. Hermione and Ron are polar opposites, and despite the saying, there is no way they would be good for each other. Hermione is driven and her ambition/work ethic is legendary. She strives to be amazing and hates flying. Ron is an admitted slacker, constantly teases and insults her, and seems to only care about quidditch. Truly awful pairing.
With Harry, he has always shied away from his fame, never wanting to be famous, always looking to be a normal guy. So obviously he picks a girl who clearly has hero worship of him, developing a crush before they had even met. Also, the basis for his attraction to her was such crap. The whole green-eyed monster of jealousy in 6th year was bs and sounds a lot like a potion. It came out of nowhere especially with almost no prior interactions. In addition, Ginny had at that point almost no personality beyond having a massive crush on Harry. ugh I hate that pairing almost as much as Ron/Hermione.
There’s a lot more I could go into on the flaws for the story. As much as I love Harry potter, and the universe, i’ve found myself kind of turned off of Rowlings work as I think about this stuff more.