Ok here is mine
Proving a woman is tough
But she is a woman and isn't meant for war and strife
Yeah, this bugs me a bit too, but I think that most games you're talking about make female party characters integral to the plot somehow, like Aeris/Aerith from FF7 or Marle from Chrono Trigger.
Then again, the only JRPGs I have are Chrono Trigger and Persona 3 Portable, so I could just be talking out my ass right now.
I don't feel like Aeris or Marle fit that. SURE Marle had to prove she is tough... but she never had to prove it to the player. We knew she was tough and we knew one of the major reasons why no one else thought she was, was because she was an irresponsible often bratty teenage princess who often shirked responsibility and went on flights of fancy.
While Aeris I guess counts... But the game is filled with so many other strong female protagonists that her femininity never stems from it. It never feels like the game uses her gender as an excuse. Sure she is a gendered archtype, but the game follows her story and easily could gender flip her without changing how the game would have handled her.
Also SURE Aeris also had to prove she is tough and FORCE Cloud to take her along... but that is because Cloud is a soldier and Aeris is a civilian... and Cloud never refuses other female help... that and Aeris sort of acts almost like a child at that point.
Heck Leon in Star Ocean 2 sort of has that aspect of "Should we really let him join our team" but puts it at a good time where "Its either that or leave him to monsters".
This occurs more often in the Tales games.