I'm only familiar with FATE from the Dresden Files ttrpg, but the system should work if adjusted for superheroes. I think the big thing would be the ability to deal "consequences" instead of HP damage. Sure, that mugger in a back alley can't scratch your Superman-alike's invincible hide, but if they manage to crit against you then suddenly a nearby building explodes into flame and the Superman-alike now needs to wrap the fight up quickly so that they can help with that. Basically the building catching fire would be the damage from the crit.
I feel like any situation in which you're talking about a mugger in a back alley being a serious threat to a superman alike is not so much a failure of the system as a failure of the GM or module, because like.
in what world do even the superheroes who are
nominally vulnerable to 'mugger with a knife' actually consider that a threat unless it's literally first day with powers type shenanigans?
When Batman or Spiderman or whoever is
meaningfully threatened by 'a man with a knife' it's because they're secretly a ninja or some such. It's dissonant if you're throwing down with people who explode buildings and then next encounter is One Ordinary Dude, Equipment; A Mundane Knife.
There's a series of sidequests in act 5 of Diablo 3 wherein a bunch of rebellious nobles are trying to pull a coup on the king, leading to the story acting as if the player is threatened by people who are, at best, mercenary wizards and mostly
literal peasants, when you're
currently fighting legions of soul stealing evil angels as the main threat of the act and have
just finished getting into a punch out with Prime Evil Diablo aka Diablo but also with the power of all the other six most powerful demons, 1v1 and winning after scything through the best legions hell has to offer and various corrupted angels.
And entirely aside the politics of whether I even
should be spending time crushing a popular rebellion instigated by a corrupt nobleman vs an inept king while Literally Every Human In The World is going to die if my main quest fails, it comes across as farce because, come on, if I can come out on top vs Super Satan, a bunch of random peasants aren't a threat to me and no I don't buy 'some noble moron with merc wizards' is narratively relevant either.
This problem is true if your superman expy is up to the point of being A Justice Leaguer Type Dude, not because 'he has invincible skin' but because if you've been prevailing against things far more dangerous that Random Muggers, your Random Mugger comes across as comedy or farce on the face of it. It doesn't matter if you
are The Incredible Hulk if you're already been throwing down with people
like The Incredible Hulk it's going to be off to then seriously act as if A Mugger is a level appropriate threat, and more off if they do in fact have the stats to outclass Doctor Magic Ray Gun, Destroyer Of Houses you fought last week.