I wasn't even aware that Bill was supposed to be gay until I've read some posts about it. And yeah, now it makes sense, and it was really subtle. So, basically the fact that Bill was gay meant nothing to the story. It didn't affect his skills, his personality, or basically, anything. He just happened to be gay. And that's definitely one way to handle that. But, on the other hand, is this the only way to handle gay characters? For example, in Persona 4, Kanji's struggle against his sexuality was cornerstone of his character, and that is one of the reasons he is held in such high regard.
So, maybe it's not about how we handle gay characters, but how well they are written.