- Mary Jane chews Peter out for missing her play, not listening to his legitimate explanation for why he missed it in the first place (his scooter got ran over by some thieves being chased by police, and he had to transform into Spider-Man to stop the thieves after they took out the police cars). But remember how Mary Jane was used to being disappointed by others during the first movie: she had a terrible relationship with her father. She broke up with Flash at their high school graduation. Harry didn't really stick up for her when his father said she only dated him for his money (we saw her reaction when Norman made that remark, making clear how much Norman's words stung). In fact, Peter has been the only person who she could depend on. In the end she finally realized who she truly was in love with, and it was Peter. But Peter couldn't be with her because he's Spider-Man. So when Aunt May, Harry and even her father showed up to see the play and Peter didn't, she probably felt a little betrayed.
- The fact that Mary Jane is in love with Peter also explains a lot of her behavior around John and why she abandons him at the altar. In that one scene with John at the party, she wants to see if she feels the same thing she felt when she kissed Spider-Man. She feels nothing. Then, at the coffee shop, it's clear she wants to try it on Peter, at least until Ock interrupts the moment by throwing a car through the window and then showing up to abduct Mary Jane. When she sees that Peter and Spider-Man are the same person, she's just stunned. She came to realize that all those times Peter was unavailable, he was out there saving people, and knew now for why they couldn't connect before. It's also important because nobody else really saw Mary Jane as a person throughout the trilogy. Nobody saw her and wanted to be with her because they cared about her besides Peter. And as much as Peter declined to be with her for her safety (given Norman kidnapped her as bait after figuring out his secret), she pushed that aside because she knows now that Peter has genuine love for her and she's willing to put up with it now and risk her life for it. Because that's what she wants to do with her life.
- The "cake scene" is often pegged as a pointless Big-Lipped Alligator Moment. Basically, Ursula invites Peter over for a slice of cake, and he sits there eating in awkward silence for a minute, enjoying the cake but not having anything to say to her. The scene was emphasizing that despite the Character Development over the past film-and-a-half, deep down Peter is still a socially awkward geek who can't relate to people. This casts new light on his relationship with Mary Jane — whom he can talk to.