Oooh, you forgot Bully/Canis Canem Edit. It had a gay romance option for each of the cliques, and managed to avoid getting its ESRB rating put up just for the fact - which I always thought was a pretty good step forward at the time, especially considering how much abuse they got just for adding a little bit of completely optional/avoidable homosexuality :/
Ugh, Dragon Age: Origins pissed me off, they made very little effort with the finished relationship conversation trees, and they were so easy to glitch. Alistar could be seduced by a male PC, and would flirt back, right until the end - then he'd just act like nothing ever happened, or could happen
I think it's really sad that the option isn't there in more games, I mean personally I don't see the big deal with just giving us the choice - it's not like we're asking for a whole market to be dedicated to us, just a little acknowledgement. After all, we buy video games just as much as heterosexuals do.
Saying that however, I think it may be a while before it becomes a common thing outside of the more progressive companies like Bioware. The gaming industry seems to be fairly geared towards straight men; women are under-represented a lot too, so at least it's not a problem
just for us, although obviously it's a bit more severe for us. But saying that, at least we don't need to be made sexually objectifiable objects before we can be considered protagonist material
So... my point would be, I think in general gaming is a fairly exclusive medium - probably because of the money that goes into it these days; and therefore the requirement to be commercial, and as casual as possible (watch how much simpler Fable got from 1 to 3 and you'll see my point -_-). I guess they think things like female & gay protagonists are just too risky a move, unless they're justified by being sexual objects, or comic relief.
Luckily there are companies like Bioware who have the common sense to see that that kind of pandering isn't the only route to success :3
I'd say that indie gaming could help bring these issues out of the mainstream, but the problem is they need this easy-digestibility even more than big-name games if they want to be succesful, so pulling that kind of "stunt" would probably be a bad move for a fledgling company.