I suspect when it comes to depicting superhero characters (or any ‘super’ character really), there’s a fine line between giving them flaws whilst making them idealised and making them actually fallible as to be infuriating and disappointing if because they’re the ones you trusted a lot. I know that feeling too and it still stings me to this day. But at other times it’s a Sophie’s choice between a disappointingly fallible character and a Mary Sue.
I guess it’s going to be hard trying to come up with flaws for characters because you want them to be likable but at the same time they can’t be Mary Sues either. A balance’s possible. But not when some situations demand a Sophie’s choice that it’s ultimately going to piss off readers either way. It’s not so much that liking superheroes is bad but it’s either a fallible of accepting fallibility or at least hoping for real improvement because you feel disappointed.
The latter at least allows character development but I think that’s best pulled off in The Secret Garden and Jojo’s Bizarre Adventures and Yu Yu Hakusho to some extent where I think a delinquent turning into an upstanding hero’s more interesting than say a glorified fan surrogate (I’m looking at you Tim). But that’s something not too many superhero writers actually do with reader surrogates.
If because it not only makes them too human but also take on a mind of their own so it’s a Sophie’s Choice 22. It’s going to be a tough act to do anyways.