Inverse Logic!
Valkyrie Profile - Shows that a woman is only good and strong if they work for a man, Lenneth for Lucian and Freya for Odin.
Odin Sphere - Shows that even strong women are weak. Gwendolyn as powerful as she is, is taken and forced to marry against her will, and given away as an object.
Fatal Frame - Shows that women are too stupid to realize that ghosts are not real.
Metroid - Shows that a woman's only good as a mother in the end. Samus takes in the alien.
Pokemon - Female characters second to the main male character. It's only recently that this isn't the case! Feminism for the win!! woo and yadda yadda yadda
Final Fantasy Tactics - Damsel in distress. Agrias is useless and lets the princess get captured. Agrias relies on Ramza to try to save her. Ovelia, and Alma both get captured. Teta is captured and killed, and abandoned like an object.