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.
A fairly minor example can be found towards the thief who killed Uncle Ben. Was his decision to throw Peter his milk a small Pet the Dog moment, or was he simply trying to bribe Peter into silence while he stole money from the register.
Other changes to/interpretations of comic lore (regardless of the reboot premise), such as not having Peter as a wrestler and the greater emphasis upon Peter's parents as part of a Myth Arc (Peter's parents have generally always been controversial.)
The changes done to the origin story. The fact that Peter acquiring his powers was pre-meditated by Oscorp and not an accident. The fact that the origin story never really concludes. Heck, the fact that the origin story is even being re-told at all!
"You found my weakness, it's small knives!" is reminiscent of "A bullet came out of his gun somehow! How did he know my one weakness?" from these parodies of the Spider-Man newspaper strip floating around the Web since 2004.
Much laughter was had when the first leaked production photos were of the car thief scene, strangely involving Spidey and said car thief in... suggestive positions. Now we know that the crotch thing was deliberate.
It's the Same, Now It Sucks: The main complaint of film critics who didn't like the movie that it's too similar to Raimi's Spider-Man: the origin takes up the full first hour and then the film shifts gears to Spidey facing a crazy green villain, even ending with a funeral at a graveyard.
For some reason, Avi Arad, executive producer for the Spider-Man film franchise, tried to say that this film doesn't erase the previous films and can fit into the Raimi timeline. Some posters even referred to this movie as "The Untold Story". Anyone with so much as a functioning brain cell can see that this isn't the case and this film is indeed a reboot.
The focus on Peter's parents in the marketing, which is part of a Myth Arc that doesn't actually have much impact on this movie's plot.
Narm Charm: The crane scene. Some have compared it to the scene where New Yorkers throw garbage at the Green Goblin in the original Sam Raimi film.
Never Live It Down: One thing that, evidently, a lot of people can't get past is Peter's comment that promises you know you can't keep are the best kind, which hints that he'll continue dating Gwen regardless of what George Stacy told him while on his death bed. That it's literally the last thing said and done in the movie doesn't help.
Gwen too for some for knowing this and yet still encouraging Peter to break said promise to her own deceased father. Even so, these people still don't look forward to the inevitable consequence for this to befall Gwen.
The nerdy girl who had her banner ruined is this. She flips out on Flash, saying he threw his basketball and knocked over her paint intentionally. Except: 1. It rolled into her paint, which would be a pretty dumb way to go about doing that. 2. It's a banner for his team. And 3. She decided to paint next to an ongoing game of basketball. Sure, he acts like a Jerkass afterwards, but he was just accused of something for no reason.
Visual Effects of Awesome: One thing many agree on, the web swinging looks fantastic. The shot where Spidey is wrapping the Lizard in a great layer of webs is a tad... conspicuous, however.
What The Hell, Casting Agency?: Casting a then 28-year-old man (Andrew Garfield), to play a highschool teenager falls here for some. Tobey Maguire was about the same age when he was cast and that is rarely brought up (probably because Maguire's Spider-Man was a teenager for only the first third of the first film and old enough to go to college in the subsequent films), but it doesn't exactly help Andrew's case either. However, it can be forgiven; does he reallylook like he's 28◊??
Don't like that Beenox altered the suit from the movie by adding a utility belt? The first time the player heads to Peter's apartment, they have the option of removing the belt from the suit, pleasing those who like both versions of the suit. Don't like either version of the suit and wish it was the one from the previous trilogy? That one's unlockable too.
The Wii nor 3DS got the Wide Open Sandbox that was on the other versions, and most sources didn't really bother to point out the Wii version didn't have the Sandbox world. Around March, a Wii U version was released with the entire Wide Open Sandbox and DLC packs already in the game.
The change in the suit from the one in the movie, with Beenox adding a utility belt to the ensemble. Resulted in the Author's Saving Throw mentioned above.
Harsher in Hindsight: In interviews promoting the game, Beenox pointed out they needed to get the film's producers approval on what elements & characters they used & referred to in the game, to avoid using anything planned for future films as the game was supposed to be canon to the film. The Amazing Spider-Man 2 wound up using Rhino, Felicia Hardy and Alistair Smythe in the film, completely contradicting the use of those characters in the game.
The inclusion of the costume from the previous trilogy as an unlockable extra became this, after the first shots of Spidey's costume from Amazing Spider-Man 2 revealed... that it's more or less replaced the costume from the first film.note "More or less," because the eyepieces & the Spider insignia on the chest are different, and the webbing is black instead of the silver on the Raimi suit.
What The Hell, Casting Agency?: Sam Riegel as Spider-Man instead of Andrew Garfield, after Tobey Maguire voiced Spidey in the three tie-in games based on the trilogy he starred in. Note that some are noting that Riegel would actually make a rather good Spider-Man, if he wasn't standing in for the star of the movie. There's another camp who questioned why they didn't have fan favourite Spidey voice actor JoshKeaton, or even DrakeBell, reprise the role.