Caveat gamer: This idea has never been tested.
Suppose that super powers kill. You basically have a choice: low power and you'll live a long time, or high power and die quickly. Powers are a gift from some other source, a kind of "power-hours" if you will. It might be that the use of powers creates paradox that backlashes and kills you, or that it puts an aging strain on the body that adds up over time.
(Mechanically, I'd figure some way to hook power levels and frequency of use as paradox--call it "burnout"--and roll death for your next adventure. If the player botches the roll, he or she is obliged to die in a spectacular fashion in the next adventure. You could work some way for them to escape that--some kind of trouble voluntarily taken on--but so long as you're up-front with your players about the set-up, I don't think there would be a problem.)
I'd probably use a long storyline as an arc: the mystery of the immortal villain.
He's lived a double lifetime, and Ballard is his name. --Logan's Run, the book
So why would someone be immortal in this set-up?
(Yes, I know they have the Immortality power, or Immunity to aging, or however your game defines it.)
With these rules, what would justify immortality?
Maybe the power is to possess someone. The possessor wears the same costume each time, and when that body is used up, moves on to another one.
Maybe it's cloning--it is a clone taken from the original body, kept in stasis when he first got his powers, and the clone, like a remote drone, is sent out to do the work. (That implies an organization of some kind. Someone who has cloning technology came up with this scheme.)
Actually, thinking about it, maybe the suspended animation, the cloning, and the mind copying are all low-level powers that work only because übervillain is going along with it. They all share in the loot that übervillain collects.
The break for the players comes when the bad guy has a unique experience that changes his heart--and he doesn't return to the base. Now there are two übervillains, though one is trying to make amends. But he daren't use his powers, or he'll die--he's that close.
And to take the bad one on, the players have to ramp up their powers to the point they're going to die...