Like I said before, it’s not that characters like Kitty Pryde lack flaws as much as writers and readers tend to be blind to the person she really is in comics at least until recently. Whether or not she’s a Mary Sue’s up to anybody’s guess but the big problem’s that even if superhero comics do require suspension of disbelief, Kitty Pryde wounds up being too ridiculous to be believable.
That’s if she’s supposed to be a normal girl, it wouldn’t make sense if she’s depicted as a massive hacker and ninja with a pet dragon. No wonder non-comics adaptations drop this. That and no real limitations to her phasing power (from what I’ve heard of).It’s not that there’s anything wrong with fantastical characters.
I think Jojo’s Bizarre Adventures has a good way of depicting superpowered characters with believable consequences and limitations for what they do. Hurt the character’s familiar, you also hurt the user itself. Josuke gets mad, his stand can’t fix things right because of it. Rohan Kishibe annoys Josuke enough to have him be beaten up.
Dio Brando’s capable of stopping time for only 9 seconds but puts it to good use when throwing knives and so on. (I might be cherry picking as there are some characters exempt from this.) But at least it feels more believable than amping characters’ existing powers up without any consequence or limitation at all.
Not that JJBA’s any better but that a good number of works (superhero or not) really don’t bother giving characters reasonable flaws and consequences. It’s not always a matter of how scientifically accurate it is but rather a matter of making believable or otherwise it doesn’t make sense at all.