-The Sinister Six seems llke an obvious way to go. Or maybe merge it with the Master Planner framework? If only to show that image of Spidey under the rubble in the flooding lair.
-a moment where Flash Thompson gets wrongfully attacked while wearing the Spidey costume?
-"Face it, Tiger. You've just hit the jackpot."
-re-attempt the black suit/Venom story
- this leads to an eventual Agent Venom, maybe? Or Carnage if, y'know, they wanted to really dig into the bottom of the barrel...
-Scorpion? Alongside the Spider-Slayers?
-Prowler?
-Black Cat?
-Jackal and.... clones...
-a crime-centric story vs. Tombstone (as a stand-in for D'onofrio's Kingpin)
-Kraven's Last Hunt?
The tricky part is not all of these really affect Spider-Man really personally to create a real arc on their own. Someone like Scorpion or Mysterio could be cool to see, but it's also too easy for them to simply be villain-of-the-week type antagonists, making the movie simply feel episodic which is something the lesser Marvel movies get heavily criticized for. And typically, Marvel movies have far less-commonly sold their movies around the antagonist. Ultron, Loki, and Winter Soldier are maybe the biggest exceptions.