Juggling Male/Female Character Dynamics

Here is a suggestion that has works very well for me:

The Draft Story. I have an idea of the characters who are in my story, but, I really don't know who they are. The draft story is the play box for my characters and other elements in my plot. I just start writing, and see where the characters go and how they develop. I think of it as just letting the blood flow along the bones of my plot and fleshing things out.

Here is an example of the development you are wanting to see:
I had cliche bad-ass-gravel-throat-killer out to revenge the murder of his wife team up with my protagonist, innocent girly-girl who is the daughter of an evil god. My plot had her sort of falling in love with him but, him being the noble-bad ass, turning her down. Eventually, he sacrifices himself for her.
In the draft story, the two had so much chemistry that eventually I surrendered little by little not only to the romance but the two actually married. The reason for the chemistry? Girly-girl has been secretly training her entire life to kill. The people who she grew up with are horrified by her. The killer? He eventually sees a soulmate. He loves the woman that she has been hiding from the world and, frankly, isn't upset about it. While he is a broken man driven to kill out of vengeance, she turns out to be the real killer of the two.
Oh, and he still dies. Horribly.

It's meat like this from my draft story that really turned by plot and character into a story that I enjoyed writing.
Hope it helps.
Godspeed!