Raven Xavier Kitari
Pinkie Pyro
Raven Xavier Kitari
Super Princess Peach, Alien Syndrome, Resident Evil 0 (half the team was female), Resident Evil (play as Jill), Resident Evil 2 (play as Claire), Resident Evil 3, Resident Evil Code Veronica X, Darkened Skye, P.N. 03, and Demon Blade Muramasa
Those RE games are all Capcom though. I wouldn't count them.
Still counts. Female protagonists were asked and capcom delivered quite a few
Sure... if you ignore what the OP actually said when they said "By Nintendo games, I mean games that are published and/or developed by Nintendo."
You know since that means Capcom games do not in fact count for what they are asking for... since Capcom developed and published them not Nintendo.
That of course also means P.N 03 does not fit criteria (Capcom developed and published that as well), nor does Darkened Skye (Boston Animation developed it and depending on region either Simon & Schuster, TDK Mediactive, or Oxygen Games published it), neither does Muramasa: The Demon Blade (that was developed by Vanillaware and published by Ignotion or Aksys in NA depending on platform and Marvelous in Japan), and neither does Alien Syndrome (That was developed and published by Sega)
which leaves out of all of those.... Super Princess Peach as the only game that actually fits what the OP is asking for.