• 3 has a transphobic scene in it that was corrected in 3 Reload (remake)
• 4 is a mess for a lot of reasons. there's a character who occasionally says homophobic things to another character throughout the game. that character was literally supposed to be bi and they even had dubbed audio for it that was data mined, but it was inexplicably remove late in development. the character who has homophobic things said about him turns out to have an ambiguous sexuality instead of outright stating bi, when it was very obvious the intent they were writing towards. there's a character that was written in a trans way but isn't trans and they lean into some more traditional gender stuff with them late game. I'll leave that vague, because I really think their story is more complicated than meant to / not meant to be trans. it was poorly handled no matter what tho
• 5 has a homophobic scene that they attempted to improve in 5 Royal (re-release with new content)

in 2 you can literally choose a gay relationship canonically without issue. that game came out in 1999 lol