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Start by understanding that a girl with super-powers is a girl just like any other girl except with added super-powers. Then understand that it is perfectly normal for girls to be capable and comp...
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#3: Attribution notice added
Source: https://writers.stackexchange.com/a/44259 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
Start by understanding that a girl with super-powers is a girl just like any other girl except with added super-powers. Then understand that it is perfectly normal for girls to be capable and competent. And that those are qualities you learn from experience. So your characters would over time grow to be capable, competent and confident. Gender actually has no impact on this. You probably should acknowledge that we live in a society where it is still somewhat awkward for young women to **express** being confident and capable. There are studies that suggest that in subjects such as maths girls do worse in mixed groups. Incidentally this is also not specifically a gender issue. It is part of the process of growing up and building up your adult self. Both genders actually have the same issue. The difference is that boys are specifically told they should be confident and "man up". The role models for girls that are pushed otoh... Fortunately you can solve this fairly easily simply by providing your girls with some adult women they can look up to. This moves your issue from characters in focus to background characters. Your main characters would not really need to know or care if these role models fit into the trope, so you do not need to show readers either. So I'd go with ordinary girls with super-powers, normal growing up issues with self-confidence, and good role models. Then show them organically growing into whatever you wanted them to be without changing into another character. That incidentally is a common issue with these types of stories. If you start with the super-hero and then insert "the backstory", it is very easy to end up with two different characters. So you should make sure that the pre-powered character has enough development that carries over. Classic Spider-Man is probably the best example why this matters, it is actually Uncle Ben and Aunt May who made Spider-Man not a radioactive spider. (And that one selfish moment that makes certain that making Spider-Man give up is well beyond the reach of normal super-villains.)