And really I think this is an artifact of the way (predominantly male) creators think about characters. The unmarked state, the prototypic clay from which characters issue forth, is a white straight male. Characters get traits slapped on to this base form to create a diverse cast, but the relationships are still generally protagonist-centric and prototype-centric. Even when there's a strong character who is a woman, she's probably going to have relationships mostly with male characters because she's the Other, the object, and it feels intuitively more probable for her to be connected to the subjective norm than to another Other. Even icons like Alyx Vance or Elizabeth from BSI fall into this trap.
It's like writers approach cast design the way they'd approach a D&D party - we need one of each class, where the classes are 'normal', 'woman', 'black', and, odds are, 'different normal'. Other configurations feel somehow improbable, and people even accuse them of 'Political Correctness' (whatever this means).