I would say (hands down) MEGS (aka DC Heroes RPG/Blood of Heroes), except that you said it can't be dead.

I actually think that system is as good as or better than the HERO System for supers. (Though the way it handles scale keeps it from being a good universal system like HERO is.)
Unfortunately, I don't have enough recent experience with other games to be too helpful. M&M seemed pretty decent, but I haven't looked at 2nd or 3rd editions. Silver Age Sentinels was good, but long-dead now, AFAIK. GURPS has always felt a little clunky to me for supers; it doesn't feel like the powers system integrates too well with the rest of the game system (although I think it's much better in GURPS 4E than in previous editions).
For a game that would have an entirely different feel from the HERO System, but maintain the flexibility (albeit in a very different way), you might look at very freeform game systems like FUDGE, or even RISUS. You'd probably need a lot of GM-player trust and agreement about the goals of the game to make those work well for supers...
EDIT: I've also heard good things about Truth And Justice, though I don't have any experience with it myself.
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