I thought he was actually used quite well. Certainly, I wasn't expecting much and he surpassed expectations.
I think the story should start small scale, which is why I want one of Spider-Man's semi-fantastical street level villains involved in some way: Hammerhead, Tombstone, Enforcers. Since every Spider-Man story seems to be about how great power comes with great responsibility, it's hard to pick something that a particular villain would be suited to. Since he's in High School, I could see some kind of theme of youth, but that's just an excuse to say that Vulture (and maybe Silvermane) should be in it.
If it's tied to Civil War, maybe play on the idea of the world against Spider-Man and consider the Spider Slayers. Although, if the slayers end up sanctioned as part of the government actions (as a Civil War storyline would imply), that comes a little too close to a Hulk story (Hulk vs. the government).