Many of these things need to be put into context, not to mention the historical context and culture of that time period.
Let's start with the Genesis reference:
Gen 2:24 Therefore shall a man leave his father and his mother, and shall cleave unto his wife: and they shall be one flesh.
The following is an accurate understanding of the duties men and women had/have to each other:
Eph 5:22-31 Wives, submit yourselves unto your own husbands, as unto the Lord. (23) For the husband is the head of the wife, even as Christ is the head of the church: and he is the saviour of the body. (24) Therefore as the church is subject unto Christ, so let the wives be to their own husbands in every thing. (25) Husbands, love your wives, even as Christ also loved the church, and gave himself for it; (26) That he might sanctify and cleanse it with the washing of water by the word, (27) That he might present it to himself a glorious church, not having spot, or wrinkle, or any such thing; but that it should be holy and without blemish. (28) So ought men to love their wives as their own bodies. He that loveth his wife loveth himself. (29) For no man ever yet hated his own flesh; but nourisheth and cherisheth it, even as the Lord the church: (30) For we are members of his body, of his flesh, and of his bones. (31) For this cause shall a man leave his father and mother, and shall be joined unto his wife, and they two shall be one flesh.
It's quite dishonest to imagine a woman slaving away under a domineering husband, when abusive relationships were condemned in both Christianity and Judaism.
Regarding the "rape punishment," while Deuteronomy does not mention it, the Father's consent is required for the marriage, and is probably assumed as self evident in Deuteronomy:
Exo 22:16-17 And if a man entice a maid that is not betrothed, and lie with her, he shall surely endow her to be his wife. (17) If her father utterly refuse to give her unto him, he shall pay money according to the dowry of virgins.
Ancient Jewish commentators expands this as saying that the daughter also ought to consent to the marriage, though the Father is ultimately in charge. It's also worth noting that the fine is on top of the traditional dowry, and does not replace it.
The premise of the law is that if a man rapes a woman, he must take responsibility for her and has no option of ever divorcing her. I liked Gill's Exposition of this passage:
"Then the man that lay with her shall give unto the damsel's father fifty shekels of silver, For the abuse of his daughter; and besides this was obliged to give her her dowry also, as Philo (d) says, which is commonly said to be fifty more:
...and she shall be his wife; if her father and she agreed to it; and in such a case the man was not at his liberty to refuse, be she what she would, agreeable or not, handsome or ugly; he must, as the Jews express it, drink out of his pot, or marry her, if she is lame, or blind, or full of ulcers (e):
because he hath humbled her he may not put her away all his days: to all the other parts of his punishment, paying a fine of fifty shekels to the damsel's father, a dowry of the same sum to her, obligation to marry her whether he likes her or not, this is added, that he is not allowed to divorce her as long as he lives; which was permitted to other men, and this was wisely ordered to preserve chastity.
(d) De Special. Leg. p. 787. (e) Misn. Cetubot, c. 3. sect. 5."
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While it is true that women who were not virgins upon marriage were stoned to death, men who raped married women or virgins who were engaged were stoned to death. In those days, men and women were expected to live up to certain roles, and there was no mercy for a man who committed heinous crimes.
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Regarding brothers marrying the widow of a deceased brother. The premise is that if the brother had no offspring, the first child of this new union is accounted as the first son/daughter of the deceased. Hence, this person is able to inherit the property of the dead brother. It's also a protection for widow's, as it is easier to be married than to be a widow.
While the quote there says "son," daughters also were eligible to inherit property if there was no son:
Num 27:1-8 Then came the daughters of Zelophehad, the son of Hepher, the son of Gilead, the son of Machir, the son of Manasseh, of the families of Manasseh the son of Joseph: and these are the names of his daughters; Mahlah, Noah, and Hoglah, and Milcah, and Tirzah. (2) And they stood before Moses, and before Eleazar the priest, and before the princes and all the congregation, by the door of the tabernacle of the congregation, saying, (3) Our father died in the wilderness, and he was not in the company of them that gathered themselves together against the LORD in the company of Korah; but died in his own sin, and had no sons. (4) Why should the name of our father be done away from among his family, because he hath no son? Give unto us therefore a possession among the brethren of our father. (5) And Moses brought their cause before the LORD. (6) And the LORD spake unto Moses, saying, (7) The daughters of Zelophehad speak right: thou shalt surely give them a possession of an inheritance among their father's brethren; and thou shalt cause the inheritance of their father to pass unto them. (8) And thou shalt speak unto the children of Israel, saying, If a man die, and have no son, then ye shall cause his inheritance to pass unto his daughter.
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As for concubines and polygamy. While it is true these things were practiced, they were one of those things which deviated from the norm of God's creation and was tolerated "for the hardness of their hearts."
Here is Christ on the topic. Though it is applied toward divorces, it can be applied towards polygamists as well due to their "marrying another."
Mat 19:4-9 And he answered and said unto them, Have ye not read, that he which made them at the beginning made them male and female, (5) And said, For this cause shall a man leave father and mother, and shall cleave to his wife: and they twain shall be one flesh? (6) Wherefore they are no more twain, but one flesh. What therefore God hath joined together, let not man put asunder. (7) They say unto him, Why did Moses then command to give a writing of divorcement, and to put her away? (8) He saith unto them, Moses because of the hardness of your hearts suffered you to put away your wives: but from the beginning it was not so. (9) And I say unto you, Whosoever shall put away his wife, except it be for fornication, and shall marry another, committeth adultery: and whoso marrieth her which is put away doth commit adultery.
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Regarding ancient slavery. This was not in any way similar to the slavery practiced by our own peoples. In those days, a slave was more like a servant, who for one reason or another (debt?) was required to serve a master for a certain amount of time. These slaves were released after 7 years.
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Regarding taking women as a prize of war. Technically, it wasn't just like having a concubine. The law required that, if they desired such a woman, that they would have to commit to marriage, with all the obvious requirements that entails. Except of course for paying a dowry, insomuch that the father was probably dead.
As for mass slaughters in general. Such events were never done for no reason at all, but were in response to some evil act. For example, human sacrifice, or previous crimes against the Jewish people or God.
I could go on, but these things must be weighed keeping in mind their context and the fact that this was in ancient times. They were more worried about not starving to death, being killed in a war, and insuring the survival of their immediate family than they were the glass ceiling.
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and they communed with her.
