@lanodan Indeed! I think the reason is because players felt more comfortable shooting men. Valve said they were careful to cover the faces and distort the voices of any human combine soldiers so that it didn't feel like you were shooting human beings.

Thematically, I think it also fits well with the feeling of sterility. (Famously, that's also why classic Star Wars has an all-male Empire.) People in Half Life 2 can't reproduce because of some evil dampening field technology, and it's implied that it's sexual dysfunction rather than mere infertility. (One to the Combine dispatch calls promises soldiers "non-manual sexual stimulation" as a reward for catching Freeman.)