You know I wonder if this movie should be three hours long and cover a good year or two of Peter's life. The villains could be the Green Goblin and Doctor Octopus, and they could tell the whole story of Captain Stacy being killed by Ock, and Green Goblin killing off Gwen.
Make Goblin look more like the comic book and have Ock act more like his comic book counterpart. In this kind of story I think there would even be room for the Vulture. He doesn't actually have to be a main character though. His time in the movie could be kind of short lived. He could be introduced partway through the movie, right after Pete becomes a hero, and defeated very quickly, and then never heard from again. do that instead of showing him beating up a common regular thug.