Of course the classic tricks in a Supers game still apply for villian teams:
'The Doppleganger Gang' (please dont' actually use these names!
) where the baddies are nothing but thinly disguised reversals of the main team: Super-Flying Guy vs. Super-Flying Bad Guy, Speedster v. Dark Speedster, et al. (Examples:
Earth-2's anit-JLA the Crime League or America (or similar, I forget its exact name) is a canon example.)
'The Antithesis Squad' take the strengths of each hero,and build someone with the exact opposite strenghts and/or the ability to counter them. Hero Fire-Elemental, meet Evil Icy Chick... Super-strong hero, prepare to face the Evil Smart-Guy! (Examples:
Numerous. Batman's Joker, and Supes' Lex Luthor are extreme (if subtle) examples. The old Namor/Human Torch rivalry is a more primal one: water v. fire.)
'The Traitor' an oldie, but a goody, have an NPC or ex-PC that has been close to the party for a period, and have some Personal Tragedy of Major Impact© hit them hard... causing them to join forces with the enemy! Can turn any minor enemy group into a huge nemesis. NPC love intrests or popular PC characters (now retired to NPC status) work best. (Examples:
(ex-PC) X-Men's Colossus joinign the Acolytes after his sister's death. (NPC) Harry Osborne becomes the second Green Goblin. (NPC) Any story-arc where Sue Storm/Lois Lane is brainwashed, or otherwise coerced into become a super-villaness. (Bonus points if heros/reader are convinced that it is because she truly loves the villian!))
'A World Which Hates And Fears Them' nothing quite clicks with teenagers better than that feeling of alienation- this is why the X-Men sell, and always have at least one teen-team book, afterall. The plight of mutants as metaphor for Blank-ism has held up for 40+ years... witch hunting baselines with quasi-governmental funding (and maybe Robots... No! Make it Giant Robots!) are always a popular option. Hordes of mooks, handful of henchmen, and a mastermind with a glass-jaw and diplomatic immunity.