I'd base it on The Spectacular Spider-Man series, and build up to the Sinister Six. Made a rough outline below
The Spectacular Spider-Man would establish a teenage Peter (15-17) who has been Spider-Man for a few months. The film would introduce Gwen, Harry, Flash, Liz, The Bugle, JJJ, Betty, Aunt May, etc.. Would also open with Spider-Man taking down thugs Flint Marko, Alex O'Hirn, and Herman Schultz. The latter becomes Shocker, and The Green Goblin is the main villain. At the end of the movie Dr. Otto Octavis becomes head of Oscorp, and MJ is introduced.
The Spectacular Spider-Man 2 would open with Peter taking down the Vulture, who he traces back to Oscorp. Would deal with the mob as well as Oscorp, with Doctor Octopus being the main villain, with Hammerhead and / or Kingpin on the side. Black Cat would be introduced, and she would pair up with Spidey but eventually part ways. Peter would hook up with MJ, and grow further apart from Harry and Gwen. At the end of the movie he graduates high school.
The Spectacular Spider-Man 3 Parts 1 + 2 would deal with the return of Norman Osborn, and the mob paying for 'super villains' to be created to take down Spider-Man, leading to the creation of Sandman and Rhino. Norman would reveal his plan to tear Peter's life apart, killing Gwen (whom Peter never fully gets to reconcile with) before releasing Doc Ock from prison to assemble a team of super villains. Doc Ock, Shocker, Vulture, Sandman, Rhino and the Green Goblin form the Sinister Six, and are eventually stopped when Spider-Man teams up with Black Cat. The Six are eventually defeated and imprisoned, and Harry inherits Oscorp.