I believe I have stumbled upon 3 characters off the top of my head that would be my favorites.
Selan(Lufia II: Rise of the Sinistrals): Defeating most every trope about a female party member in the 90s, Selan is a favorite. Not only is she not a damsel in distress, she's the commander of a royal army. She is chilling, perhaps even cold at first to the party... to an almost impractical, but strong standard. Just as quickly, her character evolves and she learns to trust more through one HUGE plotpoint in that game(I won't spoil it), and she opens up to the entire party with the same amount of strength and dedication.
Rutee Katrea(Tales of Destiny): What a 1-2 punch. Or rather, woman and Swordian. You meet Rutee as claiming to simply be a thief, only into it for her own sake, etc. What you don't know, is that she is helping people out with their lives, and that not all is what it seems with her(especially not her backstory). Her dialogue is absolutely entertaining, and it's always refreshing to see a female character that can hold their own. Atwight also provides a nice balance to the duo, playing the straight woman to Rutee's "charm" with dry and wry remarks.
Terra Branford(Final Fantasy III/VI): I believe Terra is my favorite character from the list. In early FF games, I felt like female characters kinda took a backseat at times, but the ones that were developed shined so much. Prior to this in the US, we had at least Rydia of FFIV, but not yet Reina and her sister in FFV. FFVI was the first time that I had seen a female show up as my first party member as a child. It was a huge impact. I couldn't put the game down. The crowning moment- Terra learning to feel all over again. Not understanding why she had magic, not getting so much. Then, we hit the second half of the game after a dramatic transformation, to find her caring for numerous orphaned children and truly finding her human side ironically via the full release of the esper one. She is the battle from earlier in that game's plot coming to an end, simply because the two parties involved had unified into one woman with the strength to hold up many.