Certain core themes can be universal regardless of the couple involved..
I agree, though, that the commercial landscape is such that games with a fixed narrative involving, for example, a gay couple, are going to be very rare. But the beauty of games is that we should be able to control the story. Whereas you may follow a "straight" love story in your game, someone else might follow a gay one, in the same game. Some games are very open-ended, and they should allow for a choice like this. One of the ultimate goals I see many designers preach about is to provide a game where the player truly creates the story.