Exactly. At least part of this needs to feel like you get to be Superman. And that means some stuff shouldn't hurt you.
That being said, I do like the idea of Mxy showing up for a bit - and while he's there, you can see him enchant random henchmen and make them just a crazy threat until he's gone. THAT would be cool. But anything else feels like N64's "Superman is weak and slow and you can't see too far ahead because of Kryptonite fog.... it has nothing to do with the fact that the programmers aren't great and the N64 can't handle draw distance.." It's been done.
I love the idea of a Superman game being something different like this. S:TAS on Gamecube did this a bit, but with tech being what it is now, it should be a LOT more doable.So there'd be plenty of challenges in this mission chain and plenty of bad guys who could hurt you, but it's not *just* a matter of physical defeat and you'd have a wider range of objectives and goals than just "hit the bad guy until they fall down."
Add in the reputation system I've suggested, and how you get the job done becomes more challenging and fun than just whether you can beat everyone up or not. Sometimes it should just be as simple as beating everyone up, but that's not going to be enough for a Superman game. The lore? Hell with that, what you have to worry about is the character's legend and reputation among the masses; people have an expectation for what Superman is and a game would have to account for that or risk being seen as, like I said, a generic action game with a famous name that it doesn't live up to.