Final fantasy 6, commonly regarded as the best or second best final fantasy by a large portion of the fan base, basically had two characters you could try and argue as the protagonists, either Celes or Terra. They were both women.
The actual best final fantasy game (10, fight me) basically had Tidus and Yuna, a man and a woman, as essentially co protagonists and that worked very well.
13 was a shit show, but must have sold well since they made it into a trilogy. Lightning, a woman, was the protagonist of the first and third games, and her sister Serah shares the protagonist slot with some boy as co protagonists for the middle game in the trilogy.
Final Fantasy has had very good success with games featuring women in prominent roles previously, Its a shame they are so hooked on entirely male driven games lately but for all the faults we could point at Final Fantasy games, I don't think it could be argued that they ignore women in general even if the last one was a boys club. I don't know of a lot of JRPG companies honestly that would have commited to as women driven a trilogy as the 13 trilogy was. Not without going down really gross objectification paths.
