Not sure what counts as lesser-known, but if we're just counting games developed by Nintendo:
Gals:
Mona (Warioware)
Malon and Ruto (Ocarina of Time)
The girl who runs the treasure chest game shop in the N64 Zelda games
Midna and Ilia (Twilight Princess)
Princess Hilda (A Link Between Worlds)
Paya and Mipha (Breath of the Wild)
Purah and Sonia (Tears of the Kingdom) (honestly all the women in BotW and TotK are gorgeous)
Karst (Golden Sun)
From Pokemon:
Lorelei, Cynthia, Sabrina, Karen, Diantha, Juniper, Melony, Nessa, Bea, Lusamine (kind of evil, but still), female Aether Foundation grunt, Lanette, Olivia, Flannery, Janine, Mars, Elesa, Skyla, Shauntal, Gabby, Reath, Ferma, Shelly, Caitlin, Rika, DJ Mary, Phoebe, Anabel, Lucy, Valerie, Nō, Nene, Aya, Courtney (both the Team Magma admin and the grandmaster from the Pokemon TCG videogame)
Palutena (Kid Icarus)
Kumadora (Mother 3)
Sami, Nell, and Sasha (Advance Wars)
From Fire Emblem:
Caeda, Lena, Maria, Palla, Catria, Minerva, Midia, Elice, Nagi, Malice, Athena (FE1/3/11/12), Clair, Mathilda, Sonya, Silque, Rinea, (FE2/15), Ethlyn, Lachesis, Ayra, Deirdre, Brigid/Eyvel, Erinys, Larcei, Ishtar, Aida, Lahna (FE4), Linoan, Olwen (FE5), Melady, Cecilia, Brunya, Echidna, Guinevere, Idunn (FE6), Fiora, Eleanora, Isadora, Louise, Karla, Ursula, Ninian, Leila (FE7), Natasha, Tethys, Syrene, Ismaire, Selena (FE8), Titania (! !), Lethe, Nephenee, Elincia, Jill, Tanith, Sigrun, Lucia, Aimee, Leanne, Almedha (FE9), Vika, Nailah, Heather, Ashunera (FE10), Sully, Miriel, Olivia, Cherche, Say'ri, Tiki, Naga (FE13), Kagero, Reina, Scarlet, Flora, Ophelia, Velouria, Soleil (FE14), Dorothea, Bernadetta, Petra, Mercedes, Lysithea, Marianne, Hilda, Leonie, Manuela, Catherine, Shamir, Constance, Rhea (FE15)
Guys:
Sidon, et al. (Breath of the Wild) (again, almost everyone in BotW and TotK is super pretty)
Felix and Piers (Golden Sun)
From Pokemon:
Falkner, Morty, N, Wallace, Volkner, the Striaton City brothers, Bryce, Cheren, Marlon, Lance, Will, Grimsley, Piers, Raihan, Steven, Bill
From Fire Emblem:
Ogma, Navarre, Julian, Wolf, Caesar, Radd, Jeorge, Astram, Samson, Etzel, Camus, Michalis, Roderick, Arlen, (FE1/3/11/12), Lukas, Python, Leon, Conrad, Deen, Berkut, (FE2/15), Lewyn, Finn, Eldigan, Shannan, Ares, Ced, Julius, Arvis, Kurth, (FE4), Shiva, Carrion, Fred, Homer, Sleuf, Shannam, Saias, Galzus, Reinhardt, (FE5), Dieck/Deke, Rutger, Noah, Ogier, Klein, Perceval, Hugh, Zeiss, Galle, (FE6), Sain, Kent, Erk, Matthew, Rath, Lucius, Guy, Raven, Canas, Legault, Heath, Hawkeye, Geitz, Pent, Karel, Harken, Jaffar, Lloyd, Linus, Uther, Roland, (FE7), Seth, Franz, Joshua, Forde, Innes, Gerik, Saleh, Cormag, Rennac, Knoll, Glen, Lyon, (FE8), Boyd, Rhys, Shinon, Soren, Volke, Zihark, Muarim, Stefan, Reyson, Ranulf, Haar, Geoffrey, Nasir, Tibarn, Naesala, Daniel, Jorge, Zelgius, Sephiran, Kurth, Rajaion (FE9), Leonardo, Sothe, Nolan, Volug (! !), Rafiel, Pelleas (FE10), Frederick, Stahl, Lon'qu, Gaius, Libra, Inigo, Gerome, Laurent (FE13), Kaze, Tsubaki, Saizo, Hinata, Takumi, Ryoma, Shura, Niles, Leo, Xander, Shigure, Ignatius, Yukimura (FE14), Linhardt, Ferdinand, Dimitri, Dedue, Felix, Sylvain, Claude, Seteth (! !), Jeritza, Yuri (! !), Randolph, and Rodrigue (FE16)
(Believe me these could have been much longer)
Neither guy nor gal:
Xane (Fire Emblem 1)
Limstella (Fire Emblem 7)
Kyza (Fire Emblem 9)
Shez and Arval (Fire Emblem: Three Hopes)
Fire Emblem is disproportionately represented, but in my defense there are over 1000 characters by now so..... That series is a deep well of pretty people.
_________________
Diagnoses: AS, Depression, General & Social Anxiety
I guess I just wasn't made for these times.
- Brian Wilson
Δυνατὰ δὲ οἱ προύχοντες πράσσουσι καὶ οἱ ἀσθενεῖς ξυγχωροῦσιν.
Those with power do what their power permits, and the weak can only acquiesce.
- Thucydides