Probably because the boys haven't really progressed far in puberty and the girls, for the most part, have a better social climate among themselves. A lot like how girls in elementary and middle school are a lot more on equal footing with the boys. But in this instance the boys didn't have any cultural markers to tell them that they are the "dominant" sex.
It also doesn't help that Ichigo is naturally more commanding than most people, 02 is aggressive and naturally overbearing, and Kokoro is dealing with a guy that refuses to show emotion at all. Miku and Zorome are pretty much at the same level with each other and Ikuno is just a sexually repressed girl that suffered through an emotionless partnership, so naturally she wants more control.
Honestly I don't see anything wrong with the girls being a little more dominant than the guys. It makes some sense and isn't completely one-sided when you see how passive and caring 02 can be when Hiro takes the reins.