Part 1: Peter in college with Gwen and Johnny Storm. It can focus on him dealing with full on anonymity. Main villain can be Kraven the Hunter who has been hired by Kingpin to take down Spiderman. You can also introduce here Daredevil helping Spidey out. If we're heading down the route of having Ned become HobGoblin then you end the film with Pete and Gwen dating. Gwen tells him she wants to meet up with some friends she knows from MIT. Turns out these friends are MJ and Ned and of course it makes Peter panic. This whole time Ned keeps talking about a new friend he's made at college 'Harry'

Part 2: Introduce the symbiote. Have the main villain here be Scorpion. Peter spends most of the film dealing with his jealousy about Ned's new friendship with Harry which is qhay the symbiote feeds off and thus the black suit is created.