Why was Mary Jane swiftly dropped from her lead role after she received numerous poor reviews in the third film? She's never been that good of an actress - Remember in the first film, when she auditions for a soap & she's told to get some acting lessons first? And keep in mind, when she was getting the big roles during Spider-Man 2, she was dating an astronaut whose father is the editor of a newspaper & having that girl in the cast would not be a bad thing for press.
Which leads right into Fridge Logic when she's back at the jazz bar at the end. The news covering the big battle mentioned her by name - why wouldn't the agents be clamouring to cash in on that?
Considering she keeps getting kidnapped & held hostage by supervillains, they might have decided to cut their losses.
While Uncle Ben's death might not have been a financial burden to Aunt May, the Green Goblin's destruction of their house and her subsequent medical bills could have wiped out any nest-egg Ben left behind.
Why does Peter keep Harry in the dark about how his father died - even when Harry constantly obsesses and drowns his sorrows about it, going so far as to slap Peter in the face publicly for not helping him get revenge? Why does he still deflect even when Harry finds out his secret identity and accuses him of murder to his face? Because Peter himself is still guilt-stricken about it. He doesn't tell Harry he didn't kill his father, because on some level, he still thinks he did.
The genetically-engineered spider was created by combining the DNA responsible for the attributes of 3 species of Spider. We see a graphic that the strands overwrite the Host DNA of the species it was implanted in. Because Peter's DNA is Human, that's why the mutation only causes him to develop the abilities, and not turn into a Seth Brundle abomination.
There's a somewhat popular theory that Peter actually doesn't get his $3,000 for beating Bonesaw because he misunderstood the rules of Kayfabe, and didn't realize that he was just supposed to put on a good show for three minutes and lose for the audience's amusement. If you assume that the fight with Bonesaw is actually supposed to be a staged performance, several things about it make a lot more sense. Peter's "spider sense" never once goes off during the fight, as Bonesaw isn't actually trying to hurt him. The wrestler melodramatically screaming "I can't feel my legs!" is just another performer putting on an act. And most glaringly, nobody bats an eye about Peter's webbing giving him an unfair advantage, because the match is about spectacle rather than fighting ability; if it had been a real fight, Peter probably would have been disqualified the second he used his webs to climb onto the ceiling.