Shantae and the Pirate's Curse
Luigi's Mansion: Dark Moon
Shovel Knight
Dillon's Rolling Western
Ace Attorney: Dual Destinies
Mario & Luigi: Dream Team
The Legend of Zelda: A Link Between Worlds
Paper Mario: Sticker Star
Pushmo
Mario Kart 7
Pilotwings Resort
Rhythm Thief & the Emperor's Treasure...
You don't need to give every pokemon a gender; the Regis are perfectly fine genderless.
Also, basing genders off looks is dumb when pokemon like Lopunny exist, which is 50/50 for male/female.
Banjo-Kazooie
Star Fox 64
Metroid Prime 2: Echoes
Paper Mario
Luigi's Mansion: Dark Moon
Luigi's Mansion
Donkey Kong Country Returns
Shantae and the Pirate's Curse
Rayman Origins
Link's Awakening
Honorable mentions: Diddy Kong Racing, Shovel Knight, Mario Party 2, Mario Party DS, Rayman...