Could you tell us a little about your story? What's the tone? Since it's teenage, I feel like it's lighter?
I have a super hero series here on Tapas and a freaking looooove them, so I might start rambling. A lot. People said interesting stuff, so I'll try to talk filling gaps.
Starting with Bad Guys, as said by Tim, I agree. You can break or make a hero because of their rogues gallery (though not necessarily. Name a super interesting Iron Man baddie...).
What I feel you have to have in mind when designing a durable villain (because it's always cool to have some weird one offs) is that they have to thematically relate to your hero. That's true for all story, but specially for main villains. It has been said that Batman villains all represent a facet of madness, while Batman could be said to be about bringing a semblance of order to a random world. The Superman villains that are famous are all great reflections on theme: Brainiac is a different take on the foreigner, the conquerer/colonialist in this case; Zod is a dark reflection of Superman's father and heritage; and good old Lex is the opposite of Superman, an extraordinary self made man plagued by greed and jealously. If Spidey is about responsability, the Green Goblin is power unchecked. You get the idea.
You should totally read Watchmen, as pointed by awesome dawg, because it's super good and a master class in comic narrative. That said, since you hadn't read it, let me just give a little context: Watchmen is a deconstruction through and through. It's a reaction to the silly antics of 60's/70's superheroes, arguing that the genre had become stale and that these characters must evolve to survive the ever so complex world outside. Basically the whole 2000's are a reaction to Watchmen and even itself the industry is still dealing with it's shadow, with DC's current line being basically ''DC Universe vs Watchmen''. It's a really dark story about, symbolically, the ''death of the super hero'', so you should absolutely read but depending on the mood of your story, you might not want to steer too much in that direction. For stories that are less about the failure of the super hero concept and more about its potential, I'd recommend Alan Moore's nemesis, Grant Morrison, and his work on DC (All Star Superman is the greatest damn thing!!)
Don't know if you read them, but if you want to read some cool teen hero stories, I'd point you Geoff Johns' Teen Titans, Young Avengers (all volumes are great, but Kieron Gillen might have an advantage), Runaways by Brian K. Vaughan and, while not super hero stories per se, I feel like Deadly Class by Rick Remender and The Wicked + The Divine by Kieron Gillen are the best teenage stories running around today.
Also, @nixxusnibelheim, have you tried Peter Parker's Ultimate Spiderman too? The whole run is insanely good, probably the best Spidey run ever