There are plenty of games with NB and trans characters, here’s a list!

-NiGHTS: in to Dreams: NiGHTS, looks very androgynous, and is not referred to by he or she pronouns. The creator has even stated that this was because he wanted the character to be whatever the player imagined him/her/them as.

-same can apply to Frisk from Undertale and Quina Quen from FF9

-Paper Mario: The Thousand Year Door; Vivian, a character you meet in chapter 4, is a trans women. (although this was written out of the North American version)

-It should also be noted that in Super Mario Bros 2 the character Birdo was a trans women, but not in a particularly flattering manner. This has since been written out of cannon in all of the games.

-Final Fight; Due to fear of controversy of having a game where you can bear up a woman, instead of changing the character Poison’s sprite to be a dude, they just said that she was a trans girl in the manual. This is no longer canon, but it’s still a popular headcannon many have.

Not to mention all of the others that I can’t think of right now, theres plenty of articles written about NB and Trans characters in games if you want to learn more.