Historically, the only thing that's coming to my imagination is men taking over by virtue of greater physical strength and a higher propensity for violence.
If you change the biology a bit and make women stronger and more aggressive, then it's all just the same thing except the men have vaginas and the women have penises.
The main problem with that is childbirth. Women get pregnant and give birth to children, men don't. This causes the current situation of men over women in two ways.
A: Women are vulnerable during pregnancy, and have to devote a large portion of time to childcare after they give birth. It's far more efficient to simply make the men forage for food, and once humans got intelligent, the food providing men started taking over. This is pretty universal in mammals, and the main exception, the hyena, has a far easier pregnancy cycle than human women.
B: Women invest more time into child rearing. Even if the child is shunted off onto the male at birth, there's still a nine month pregnancy to get through. A man's ability to reproduce is limited only by his own fertility and his access to fertile women, and of course his ability to care for these children. There's no genetic advantage to a woman having a personal harem, while there certainly is for men.
That's not to say there no genetic advantage in having access to a stable food supply, mates with good genes, and opportunities for their offspring, but it doesn't increase the number of offspring they can have, which is a distinct difference from men.
In short, asking what would happen if women took men's role in primitive societies is a moot question, because it's not going to happen. Thankfully, we've gotten past the stage where such strict specialization is needed.