The heroes are opposed by a mysterious organization that seeks to nullify and capture the powers of each super-powered individual, and do with them...what? Create a super-powered army? Grant powers to their own members? Infiltrate governments?
Or save the world?
(Idea brought on by late night watching of The Librarians; name from The Anubis Gates, by Tim Powers.)
Not that the agents don't have powers: they do. The powers are oddly restricted, often earth-style powers: great strength, invulnerability, turning people to stone, growth, and more, but nothing that involves leaving contact with the ground: no flight, gliding, or teleport. They can stretch, but not throw.
Some very rare members know a little bit of magic (so they say) but that's always kept a low level, and those agents can be recognized by the chains hanging from their boots.
With luck, they'll stay in the background enough that the heroes won't have an opportunity to learn that the members of the League have no powers when not in contact with the earth, either through a chain or by standing directly on it. Asphalt is okay, but up in a building is not. (That means that their attacks always happen in open areas: on the field of a stadium, in a parking lot, a park, a nature reserve.
The heroes first come across them when they steal the powers of a fellow hero, rendering him normal, even though he didn't have the kind of powers you'd think of as removable: tech skills, perhaps, or something inborn. The next time, they might help, depowering one of their foes during a climactic battle that the heroes would have otherwise lost. The powers are imprisoned in a small urn with Egyptian hieroglyphics, most like a canopic jar.
Then the Antaeus League (still unnamed) comes after the heroes. (If you have a player who is going to be absent for a while, depower that character, but otherwise don't; it's not fun to be the unpowered hero in a superhero game.) There are close calls. Maybe the heroes manage to capture one of the League.
Why are they doing this? To save the world.
They have been responsible for thousands of years for keeping magic in check. Superpowers are nothing more than magic given a particular expression. If there is a clearly-defined start to the superpower age, someone got into their hideout and broke a thousand of the magic jars. (If there isn't, then the Antaeus League has its own enemies, who sometimes manage to free some of the magic.)
They are certain that if all the magic were freed, it wouldn't be superheroes any more; it would be a full-on Tolkienesque post-apocalyptic fantasy world.
And the Antaeus League member pleads with them to give up their powers.
Now, in your campaign, they might be deluded, or they might be right.
So try throwing that into your next superhero campaign.