Dys4ia would be a good one to add! It's a classic

Heaven will be mine (Pluto and Luna-Terra are trans women), Everhood (Red is nonbinary using they/it pronouns), The Binding of Isaac (Eden is genderfluid), Get in the Car, Loser! (Sam is a trans woman), Crypt of the Necrodancer (Bolt is nonbinary using they/them pronouns), Dark Souls 2 and Elden Ring (allow you to change your gender at will), Final Fantasy XIV (allows you to change your gender), Wandersong (Bard is nonbinary using they/them pronouns), Chicory (Pizza is nonbinary using they/them pronouns)
Also Kainé in Nier Replicant ver. 1.22 is Intersex not sure if that counts

@Archagent Thanks for the suggestion!

@Rowan1312 Thanks for the suggestions!

The House in Fata Morgana (not saying who cus spoilers but if you know you know)

@FranzMagitek Thanks for the suggestion!

Super Lesbian Animal RPG: https://www.backloggd.com/games/super-lesbian-animal-rpg/

The main character is a trans fox girl named Melody Amaranth: https://slarpg.fandom.com/wiki/Melody_Amaranth

@Tomoko Thanks for the suggestion!

Umineko has a trans main ANTAGONIST who is arguably more likable than the “good guy”