On the one hand, the game mechanics of Final Fantasy games tend to have built-in gender roles and stereotypes. Except for Paine and Girl Power which were cheapened by Tits and Ass and Barbie Dress-up, there's a running trend in which the guys run over and go ka-SLASH for a zillion points of damage with a sword, while most of the gals apart from Tifa go *dainty dink* for 10 points of damage, and may wipe their foreheads in relief as their battle victory move (Aeris, Rinoa, Yuna in FFX). The girls tend to be magic users and healers (not always, but more often) while the guys tend to be fighters.
Plus there's the whole Evil Sorceress thing in one form or another. (Yunalesca, Ultimecia, Jenova.)
Have you seen how many female crusaders there are? There's Lucil and Elma, Miyu. Lady Yocun was a Crusader-- I just discovered this, whoops, so much for my high priestess idea -- and so, I assume, was her Guardian who became the Sin that Braska defeated.
There's plenty of female Seeds. There's Elena. I haven't played enough FF to know if this is true for all the games, but it seems to me that while the main female characters tend to fall into traditional healer/sorceress/thief/non-heavy-combat roles (usually, not always), and the fighters and world leaders are usually guys, the military organizations seem pretty gender-neutral.
I'm not sure about this, I'm just thinking how we sometimes assume prejudices and pitfalls of our own cultures which don't necessarily exist in the FF worlds.
Or at least it's a little more complicated.