Depends on what system you're using, but I've managed a couple of thematically linked teams with SS4 (and SS3).
The character "Benefits" are great for adding flavour. I have a team of killer robots who all have the Souless benefit, making them super tough, but with little willingness to fight to the bitter end ("This conflict is no longer logical"). Aquatic would work well for an Atlantean team, Lone Wolf for something like the Suicide Squad or Thunderbolts or Boon for characters with inherent powers, the the X-Men or Doom Patrol.
Hope that helps.