She never gets mentioned in these discussions I assume because it's such a niche game and you don't meet her until the second one in the series, but without a doubt, the strongest, best representation of a woman I have ever seen in a game is Kaoru Sayama from Yakuza 2. Without question.
She is smarter and more determined than all of the men surrounding her, and has to be ten times tougher because nearly everyone she has to deal with is a womanizer, criminal, brutish mobster type. And she's not just the badass woman archetype either, she is tough, but also has weaknesses and nuance. Her dialog is extremely well-written and the romance between her and Kazuma that develops is some of the smartest, most human drama ever done in games. People think of Yakuza as just a beat em up, but there is more dialog and character building in the series than almost anything else in games.