Why would Bioware allow players to customize everything about their character except allowing for male homosexual relationships? In a recent IGN review, creator Ray Muzyka explained that "it's not a wide-open choice matrix. It's more choice on a tactical level with a pre-defined character. So they're different types of narratives, and that's intentional."
In other words, "because we said so, and we know best, that's why."
The real answer is clear: because lesbians are hot and sexy, and gay male sex is gross. That is, if you're a gamer. According to Bioware. Who clearly intended Mass Effect 2 to allow titillation for male players, but apparently did not consider the thought that some of their players might be female. Or maybe even gay men.
Well of course not! Gay men and women playing video games - don't be ridiculous!
The original Mass Effect created a minor controversy by seeming to allow a bisexual relationship for female characters, but still only allowing heterosexual relationships for male characters. At the time, they explained this away by patiently pointing out that your female character wasn't really sleeping with another female - that other "female" was actually alien, dummies! Okay so it's small and gracile and has breasts and a defined waist and talks with a higher-pitched voice. But that doesn't make it female! It's just… coincidence! That the Asari have breasts!
Dang those aliens, looking so much like human females.
The Mass Effect 2 choices only make sense if you presume a straight male player. Straight males are famously intrigued by the idea of lesbian sex. And they seem plenty willing to play female characters in games, as the stats of any given MMORPG make clear.
However, Bioware stepped in it by not realizing that not all gamers are straight males. What? No, really! And in fact, Mass Effect 2 has become very popular among gamers who are non-white and non-male, because of the ability to customize Commander Shepard's gender and physical appearance. Gamer blog Border House has a long running series called My Commander Shepard which is all about this.
Unfortunately, science fiction continues to lag behind the rest of the world on this kind of subject. Which is saddening, because it has so much potential for doing exactly the opposite. There is quite a lot of gay-positive science fiction out there, but Mass Effect and Mass Effect 2 isn't part of that tradition.
How hard would it have been for Bioware to allow male Shepards to form a relationship with another man? Would it have cost them extra, to add that fourth option? What if it was just another alien who happened to have traits which resembled those of male humans, but was still totally an alien, just in case anyone was wondering? Nope, sorry. No can do.