If you're going to include a gay story better make it a good one right? Writing homosexuality into the story would have to the environment, the background, and the culture behind it explained.
Is it just so open that no one cares and you can do whatever you want? I doubt it, there is plenty of racism, "speciesism", and sexism in the game if you listen to the dialogues of random people. The planet, organization, species, and person make a huge difference.
None of the characters seem gay at all. Except maybe Tali or Miranda. The men either have families, aren't sexually driven, or aren't set up to being "gay".
Gay or not, you still have to write a good story behind it, and it was their choice to not have one slapped on the side of their game. They got enough flak for the first one, just remember this, you know why there isn't any gay romance in this story? Look around, people still find that behavior a threat for no good reason. Whether its politicians, shareholders, or the game designers/writers themselves.
And if they don't find it a threat, how good are they at writing gay relationships that people can enjoy? Or does it just end up looking dumb and awkward?