For all your JRPG/FF bashing, one thing you can't ignore is how well they do female characterisation - and that does not include androgenous ladyboys -_-0. In my experience, the females are stong and don't rely on ***** tactics to prove their might and keep the men in check. Because JRPGs come from Japan, and so follow Japanese sensibilities, a woman is expected to be feminine as well as strong of body and heart. Here are some leading ladies that come to mind:
Ashe (FFXII)
Yuna (FFX)
Rikku (X-2, where she was one of three leading ladies)
Garnet (FFIX)
Rinoa (FVIII - though there were many aspects to her personality I hated with a passion, but she was still strong and not particuarly bitchy)
Aerith (FFVII)
Tifa (FFVII)
Terra (FFVI)
Need I go on with FF? All of their female leads (even the roster fillers) are stong women with well rounded personalities, often moreso than their male counterparts. But that's just me. And here are some non FF heroines...
Emma and Emmy (Last Remnant)
Seth (Lost Odyssey)
Koudelka (Koudelka)
Alice (Shadow Hearts)
Karin (SH2)
Shania (SH3)
Karin (Enchanted Arms - ok, she was borderline)
Kluke (Blue Dragon)
Aya (Infinite Undiscovery)
Zephie (Magna Carta II)
Kairi (Kingdom Hearts)
Japanese survival horror is also an excellent source for strong women. Let us not forget our beloved Maria. And the Zero/Project Zero/Fatal Frame series never failed to provide well rounded, capable women to head into danger.
Seriously, the Japanese have mastered the marriage of bouncy boobage with human, likeable personality. American writers have the potential - they're also likely male, which is a problem. My writing teacher was once applied as a game's writer and was turned away because she was too old and too female. And this was in Australia.
But then there are glimmers of light peeking through that prove the potential for female game characterisation in the west; I felt at ease with the women of Dragon Age; just look at Morrigan, I wouldn't call her a *****, I'd call her self assured.