My favorite JRPG characters from games I've played, yes they're probably all female:

Final Fantasy II: Princess Hilda

Final Fantasy III: Sara Altney

Final Fantasy IV: Older Rydia

Final Fantasy V: Faris Scherwiz

Final Fantasy VI: Celes Chere

Final Fantasy VII: Elena

Final Fantasy VIII: Quistis Trepe

Final Fantasy IX: Beatrix

Final Fantasy X: Lulu

Final Fantasy XI: Prishe

Final Fantasy XII: Fran

Final Fantasy XIII: Jihl Nabaat

Final Fantasy Type-0: Queen

Final Fantasy XIV: Ysayle Dangoulain

Final Fantasy XV: Aranea Highwind

Final Fantasy Tactics: Agrias Oaks

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Grandia: Leen

Grandia Xtreme: Lutina

Grandia II: Tio

Grandia III: Dahna

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Wild ARMs: Lady Harken

Wild ARMs 2: Kanon

Wild ARMs 3: Melody Vilente

Wild ARMs 4: Raquel Applegate

Wild ARMs 5: Persephone

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Tales of Phantasia: Suzu Fujibayashi

Tales of Destiny: Ilene Rembrandt

Tales of Symphonia / DotNW: Raine Sage

Tales of Legendia: Grune

Tales of the Abyss: Legretta

Tales of Vesperia: Judith

Tales of Graces: Victoria

Tales of Zestiria: Maltran

Tales of Berseria: Seres

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Dragon Quest VII: Aishe

Dragon Quest VIII: Red

Dragon Quest XI: Jade

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Chrono Trigger: Schala

Chrono Cross: Steena

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Secret of Mana: Pamaela / Phanna

Legend of Mana: Sandra

Favorite characters for the mana series are hard to come by for me. I have played Dawn of Mana and Sword of Mana.

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Paper Mario: Lady Bow

Paper Mario: The Thousand-Year Door: Jolene

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Xenoblade Chronicles: Sharla

Xenoblade Chronicles X: Elma

Xenoblade Chronicles 2: Mòrag

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Breath of Fire: Deis

Breath of Fire II: Deis

Breath of Fire III: Myria

Breath of Fire IV: Ursula

Breath of Fire V: Violet Zeno

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Legend of Legaia: Cara

Legaia 2: Duel Saga: Sharon Blade

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.hack// (1, 2, 3, 4): Helba

.hack//G.U.: Pi

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Ar Tonelico: Ayatane Michitaka (You thought it was a female, but it was I, a male!)

Ar Tonelico 2: Cloche Leythal Pastalia

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Pokemon Red/Blue/Yellow: Sabrina

Pokemon Gold/Silver/Crystal: Clair

Pokemon Ruby/Sapphire/Emerald: Magma Admin Courtney

Pokemon Diamond/Pearl/Platinum: Cheryl

Pokemon X/Y: Celosia

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Golden Sun: Master Hama

Golden Sun: The Lost Age: Sheba

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The Legend of Heroes: Trails of Cold Steel: Scarlet

The Legend of Heroes: Trails of Cold Steel II: Aurelia Le Guin

The Legend of Heroes: Trails of Cold Steel III: Aurelia Le Guin

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Musashi Samurai Legend: Fontina / Ricotta

Mega Man Battle Network: Ms. Madd

Valkyria Chronicles: Selvaria Bles

Fire Emblem: The Blazing Blade (GBA): Sonia

The Legend of Dragoon: Rose