6. Sex trauma as backstory
5. Must be a tomboy
4. Powers/Abilities are used to help male lead
3. Cannot be leaders without also being bitchy
2. Their stories always revolve around a guy (hero or villain)
1. They can't look cool without humiliating a guy
Is0bel and Gobbet from Shadowrun Hong Kong.
They hit none of those things. Glory from Dragonfall might hit one but its kind of minor when taking her story as a whole. That said, all SR characters has a pretty dark back story. It is just the world they live in. Given they are also criminals it isn't hard to imagine they have rough histories.
Here are two competent women who survived despite the odds and managed to scrape together a way of living and survive. Great characters from a great cast in a great game.
The plot revolving around a man is part true. The plot shifts focus a few times. You might be hunting a man or woman but you don't know the ultimate master mind until later and even then the gender of this person is hardly a concern.
Now that I think about it, one of my favourite female lead characters was actually my main character in these games. Gender had very little to do with it, it was mostly because the game treated your character well based on your abilities, skills and choices. The writing carried it and made me appreciate my character that much more.
Female MC in Persona 3 Portable.
Doesn't really hit any of those though you can choose to poke fun of male class members and what not.