Yeah, adolescence is weird, and some of this is guessing based on other primates. Gorillas, for example, evict familiar adolescent females shortly after puberty while welcoming strange adolescent females, which informs how we model the behavior of pre-agriculture migratory human tribes.

(I should add we don't presume that it was the same everywhere either, so it's quite possible that some prehistorical humans had different means of managing their teens than sending the boys off to wage war and letting the girls get kidnapped in kind by raiders. Once we go that far back, we have to rely on archeological data, which is very selective in the tales it tells.)

So then, there are some powerful goddesses in early Hellenism, for instance, Aphrodite (commonly a goddess of love and beauty), evolved from Astarte (Lover, Healer, Hunter, Warrior) who developed from Ishtar. In fact, when Aphrodite emerged from the sea foam on Kytherian beaches, Phoenician traders were coming to the Kytherian harbors, not only bringing goods and their own goddess, Astarte but also the modern Greek alphabet (before which the locals were using Linear B). So we have a path from Ishtar and this major poly-faceted goddess being reduced to a love goddess, who is then married to Hephaestus (the crippled forge) to put her in her place.

Also curious to me is Dread Persephone who ruled the dead and the underworld long before Hades appears on scene. (Poseidon was the Olympian in Chief, and we see part of his gig in creating biodiversity, not just all the creatures of the sea, but also those of the land). Zeus and Hades were added late in the game, and the stories we have of Persephone, specifically of the abduction of Persephone from Demeter and the thing with the six pomegranate seeds comes from a single poem. Even then, winter comes not because Persephone is gone, but because Demeter is sad about it, and stops doing her job. So Persephone's role is to be mom's co-dependent emotional-support assistant during springtime, and go back to attending the dead.

So here we have two examples of powerful goddesses that influenced the Hellenic people and culture who are then shoved backstage with the addition of Zeus and Hades.

There's a similar event that I remember from Snow Crash by Neil Stephenson regarding Asherah, the consort to Adonai / Elohim / Yahweh. Asherah was always the ambitious one between the two, and the Canaanite temples to her were bigger and more numerous than the ones to Adonai. Eventually an ideological rift developed and the Hebrews raided all the Asheran temples, massacring the acolytes and burning them to the ground. The whole don't boil a calf in the milk of its mother thing (which informs the separation of meat products and milk products in kosher diet) is a specific reference to an Asheran ritual meal, I think for weddings, but I'm not sure.

While I can't speak to whether misogyny is innate, I can say we've had periods in which goddesses were accepted alongside gods and in some cases were on top of the pantheon. We don't talk much about Gaea anymore even though in Hellenism she created everything on earth long before Poseidon was tinkering with horses. I think there's a division between Dionysian culture and Apollonian culture which parallels the shift from chthonic religion to celestial religion. (Chthonic gods are not to be confused with Cthonian gods, who are 20th century, and definitely celestial).

I can say that in the middle ages and the domination of Christianity, women were completely unpersoned and regarded as chattel beasts (despite their capacity to think and talk, both of which was discouraged). Even Mary, mother of Jesus was not even given due recognition until the 12th century.