Well I look at the theme and the development of Peter Parker as the same thing.
The theme is the moral he learns and grows up by and by the end of the third I think he is supposed to be a full-fledged adult. The villains are then related to that theme. I would say Peter's relationship comes after that and then the villains.
People really underestimate the relationship with threads like "Phase out MJ."
If there is going to be a Spidey 4 (which there will be), I think the best thing to do is to address that Peter Parker is an adult and instead of him learning a coming of age lesson, he is now learning the lessons and responsibilities of an adult. Have him and MJ not fighting but happy. Yet there is an uneasiness to this, because they know he could die at any time and it has a toll on her and on him.
He wants to take the next step but is disheartened by seeing the creation of The Lizard and how it basically devestates and destroys that family's relationship. To prove he is ready to continue forward with MJ he must find that there is salvation for Conners and protect the man-killing creature until he discovers a cure. But enter Kraven who comes to hunt the Lizard-beast that is rumored to be in the sewers. After being foiled by Spidey, Kraven takes it upon himself to prove he is better than this man in a costume who insulted his honor by defeating him.
He simply captures Spidey and without rants, dialogue or promises of joining him, he simply buries Spidey alive and takes the man's costume as a trophy and will wear it to kill the Lizard. Thus betraying the Conner family's trust in Spidey and scaring MJ who doesn't know where Peter is. She is the one who finds him somehow saves him, unburies him and this proves she won't run from him and is ready to stay the course and it allows Spidey the strength to stop Kraven and eventually cure the Lizard.
This would allow for a small wedding ceremony at the end.
Sorry that is my idea for Spidey 4, anyway.
