There's lots of gay subtext in Ace Attorney.
But when looking specifically at subtext that might be intentionally put in the narrative by the creators with the intention that the character in question is actually gay, I think the main character with the most evidence behind this is actually Apollo Justice.
Our other main characters, Phoenix Wright and Athena Cykes both have obvious subtextually heteronormative romantic partners. To an adult, straight, culturally normative audience, Phoenix Wright and Maya Fey read normatively as an obvious romantic pairing. This is also the case for Athena Cykes and Simon Blackquill. In Great Ace Attorney the same can be said for Ryuunosuke and Susato.
I repeat– to an adult, straight culturally normative audience, the romantic subtext between these characters is clear. If you showed these games to an American movie going public, that would be the obvious read by the audience.
Yes, each of these characters, Phoenix, Athena, and Ryuunosuke also have strong queer romantic subtext with another character. (Miles, Juniper, and Kazuma respectively).
However, that's not my point. It's not significant that each of the other three characters has homosexual relationship subtext.
It is significant that Apollo Justice does not have a character with whom he has heteronormative romantic subtext.
The closest thing Apollo Justice has to a "heteronormative romantic subtext" is Trucy Wright– whom we, the audience know is his sister.
And yes, you can make the argument that there is deliberate incestuous subtext between them– a kind of Luke/Leia style relationship with which the audience is teased by the narrative. Dhurke brings it up directly in Spirit of Justice.
However, this is still not a heterenormative subtext, because of its taboo nature. More taboo, culturally at this point, than homosexuality.
On top of the lack of heteronormative romantic subtext, Apollo also is on the receiving end some of the strongest and most overt of the homosexual subtext in the series.
There is of course the famous "meet cute" introduction between Apollo and Klavier–
“I must say, I'm used to being inspected by the ladies... but this is the first time I've felt this way with another man.”
This is without question overt homosexual subtext.
However, there is another, even more subtextually clearly defined moment in Dual Destinies. Honestly, the subtext is all over Dual Destinies in the way Apollo reacts to Clay Terran's death (basically completely losing it) but there's one particular moment that deliberately draws your attention to the relationship in a queer way.
In one of the last cases of the game, everyone is delicately trying to explain to the judge that Aura Blackquill was in love with Metis Cykes (who was murdered) in a queer way. It's a big “they’re lesbians, harold” moment.
And then the conversation immediately turns to Apollo Justice and how he’s just had someone who was “important to him” murdered, too.
The narrative specifically draws you attention to the relationship that Aura and Metis had, and compares it to the relationship between Apollo and Clay.
You are specifically invited to speculate about what kind of important relationship Clay and Apollo had, and why Apollo has been affected so incredibly deeply.
So yeah. Between Clay, Klavier, and the lack of anything resembling a heteronormative romantic relationship for Apollo in the games, I think he has the strongest narrative evidence that he's actually being written deliberately as gay.
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