Certainly, a superhero can be written as such. But a writer can make the assumption than the reader is fully aware of the flaws and backstory of the character and doesn’t need to be highlighted every twenty pages. THAT’S good writing.

But sometimes we get characters (brand new ones) whose backstory and current occupation don’t really ad up. The writer has just picked cool traits one after another without bothering to think how they can all exist inside one person. Most of the 90s characters seem to be mary sues in all but names. That they were later developed into real characters don’t mean that Cable, Deadpool and X-Man started out as rather underworked is hard to deny.

That there are people who don’t know how to use the terms right doesn’t mean that the term itself wouldn’t have meaning or value.

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Of course, just because the character seems to be perfect doesn’t make him a mary sue. Invincible springs to mind; the fact that he acts like a real person and not a two-dimensional model makes all the difference.