Hey!
First thing's first, your comic rocks (pun intended) and I'm adding it to my favorites as soon as I finish typing this.
My comic VERUS actually has two leads, Ajax and Ema, but she's probably the more important of the two plotwise.
I'll focus on Ema's end of the story here since we're talking about the girls. She's a scientist who was working on some very important research when her lab was attacked. Now she and Ajax have to get from Seattle to Atlanta through a wilderness infested with what's best described as zombies (but smart, fast and mutated to predatory perfection).
The story is dark and violent and kind of awful to the character at a lot of points. Both Ema and Ajax have gone through some pretty horrible things and they're both pretty young (Ema's 16 and Ajax is 22)
I used a female character not because there was any real reason for me to have a female lead, but because the character I imagined in her role just happened to be this tiny little blonde thing (she's like 5 nothing and 90 pounds). I wanted a female character who could be strong, and smart and feminine so I made one myself. Personally I feel like it wouldn't make any difference if she were a guy, but I liked the idea that I could have a girl because I don't see as many girls in comics as I'd like to.
I actually have a bunch of female side characters who feature prominantly, like Ajax's Commanding Officer, a couple of Ema's coworkers on the research and more. I try to keep my cast even and to treat the characters the same regardless of gender. I feel it gives them a better personality.