We find a very strange statement in the opening verses of Malachi.
2 "I have loved you," says YHWH. Yet you say, "How have You loved us?" "Was not Esau Ya'aqov's brother?" says YHWH, "Yet I loved Ya'aqov; 3 but Esau I hated, and made his mountains a desolation, and gave his heritage to the monsters of the wilderness." – Malachi 1:2-3 (SQV)
These words are repeated by Paul in Romans 9:6-13, when he writes about the election of the children of Abraham. But in this statement, Paul fails to explain why YHWH says He hates Esau. Even in Malachi, YHWH only proclaims the judgment and punishment that will come on Edom/Esau; He does not elaborate on why. So let's take a look at a few things and see if we can figure out just why, exactly, YHWH has said that He hates Esau.
Most Believers don't like to think of YHWH as a vengeful or angry Deity. Indeed, the phrase "Love the sinner, hate the sin" is so often repeated, that I have found many people actually think it to be a quote from Scripture itself. That's not to say that YHWH is angry or vengeful (though He calls Himself "Jealous") but He is definitely an Elohim of Justice. He will by no means leave the guilty unpunished (Exo. 34:7; Num. 14:18; Nah. 1:3). We also find a number of times where YHWH says that He not only "hates sin" but also "hates" the one who is sinning. This is a topic for another time, but suffice it to say those who choose to ignore Him and continue to live in their habitual, intentional sins: they are in a predicament which I hope to never be in.
So back on track, then. What about Esau? Why does YHWH say that He hates him? Let's go back and read a little bit about Esau himself and see if we can understand why.
19 Now these are the generations of Yitschaq, Avraham's son: Avraham became the father of Yitschaq; 20 and Yitschaq was forty years old when he took Rivqah, the daughter of Bethuel the Aramean of Paddan-aram, the sister of Lavan the Aramean, to be his wife. 21 Yitschaq prayed to YHWH on behalf of his wife, because she was barren; and YHWH answered him and Rivqah his wife conceived. 22 But the children struggled together within her; and she said, "If it is so, why then am I this way?" So she went to inquire of YHWH.
23 YHWH said to her, "Two nations are in your womb; and two peoples will be separated from your gut; and one people shall be stronger than the other; and the older shall serve the younger." – Genesis 25:19-23 (SQV)
Genesis 25 brings us up to the point where Rebekah becomes pregnant. Due to the intense struggling in her womb, she asks YHWH what's going on. Here is a very important prophecy regarding Israel and Edom in verse 23. One will be stronger than the other, and the older shall serve the younger. There's a whole teaching in that verse alone, but let's continue. Just remember: they were already striving while IN the womb.
24 When her days to be delivered were fulfilled, behold, there were twins in her womb. 25 Now the first came forth ruddy, and hairy all over like a garment; and they named him Esau. 26 Afterward his brother came forth with his hand holding on to Esau's heel, so his name was called Ya'aqov; and Yitschaq was sixty years old when she gave birth to them. – Genesis 25:24-26 (SQV)
Let's define some terms here. In Hebrew, a name is more than just something you are known by. Hebrew is a concrete and literal language, and it is not abstract like English or Latin or Greek. In modern times, we tend to give our children names that we think are pretty, or strong, or that sound good, or that are generational (passed down) traditions. But to the Hebrew mind, it is not done this way. Even some Native American Indian tribes had the tradition of changing a child's name. For instance, if a boy was named something like "Little Bird" as an infant, but was observed to be a really fast runner as he grew, his name would be changed to something like "Running Deer" after he was older. The name was given to them based on some physical trait or ability they had, and changed as their traits changed .
Hebrew names are done much the same way. They either refer to the child, or to the circumstances of the child's birth. For instance, in 1 Samuel 4 we learn about the birth of Ichabod. His mother said he was named Ichabod because "The glory left Israel." In Hebrew, the i-prefix is negative, and the word "chabod" (which is actually better rendered as "kavod") means "glory." So i-kavod means "no glory." Going through the names of the 12 sons of Ya'aqov, we find that they were each named according to what their mothers were experiencing at the time. Naphtali means "wrestling" because Rachel said she "wrestled" with her sister, and prevailed. Levi means "clinging" or "attached" because Leah hope that after his birth, Ya'aqov would become "attached" to her. All of these names are MASSIVELY significant, and we need to understand what they mean.
Esau was the first one born. It says he came out ruddy and hairy like a garment. He was named "Esau." Esau is from the root word asah which means "rough." So think of an old wool blanket, or an old garment that has been worn and is "rough" and that is what Esau was compared to. He was named that because of his physical traits.
Ya'aqov was born second. We are told he came out "with a hand on Esau's heel" and his name was called "Ya'aqov." Now just a quick glance in a lexicon or concordance will tell you that Ya'aqov means "supplanter." Indeed, this seems to make sense given what Esau says later:
36 Then he said, "Is he not rightly named Ya'aqov, for he has supplanted me these two times? He took away my birthright, and behold, now he has taken away my blessing." And he said, "Have you not reserved a blessing for me?" – Genesis 27:36 (SQV)
But when analyzing the character of Ya'aqov, and how he was chosen to be the father of the people of YHWH, we must ask: does his name REALLY mean "supplanter" as we think of it today?
Ya'aqov is from the word aqev which means "heel." Rendered literally, Ya'aqov means "heel-catcher." This makes the most sense, since the event surrounding his birth was that he came out with his hand on Esau's heel. According to some traditional Rabbinical writings, the reason was because Esau's heel was about to crush the head of Ya'aqov. As most people know (especially parents) when a baby is born, they have what is colloquially referred to as a "soft spot" on the top of their head. The technical, medical term for this is fontanelle. This spot is made up of soft membranous gaps between the bones of the skull of an infant. Since the child's skull and brain grow rapidly over the first year or so of post-womb life, this allows for the space needed to expand. After the first couple of months, the rear side of this spot closes, with the other sides following between 6 and 18 months later. However, as most physicians will tell you, this "soft spot" is especially vulnerable the first couple of months. If harmed, it can cause permanent brain damage and even death. 
So what's the point of this? Simply put, it is very possible that Esau nearly killed Ya'aqov by crushing his skull with his heel. Think of it this way: when most babies are born, they are born head first. If both Esau and Ya'aqov were coming out head first, and Ya'aqov had his hand out on Esau's heel, that would mean Esau's heel was right above Ya'aqov's head. Sure, this cannot be proven (yet) but we do have a good amount of evidence.
Next, we find an interesting statement regarding the maturing of the two boys.
27 When the boys grew up, Esau became a skillful hunter, a man of the field, but Ya'aqov was a complete man, living in tents. 28 Now Yitschaq loved Esau, because he had a taste for game, but Rivqah loved Ya'aqov. – Genesis 25:27,28 (SQV)
Esau became a skillful hunter, and "a man of the field." Now Hebraically, the phrase "man of the field" is an idiom for "worldly." Messiah Yeshua used this idiom in a number of his parables. In Matthew 13:38, Yeshua even says "The field is the world" in His parable of the sower and weeds. Yeshua didn't just come up with that, but rather used an idiom they were all very familiar with. Yeshua also said (in Matt. 9:37; Lk. 10:2) that the "harvest is plentiful." What harvest was He referring to? And what would the field be, if not the world? Rhetorical questions, of course, but you see the point.
So Esau was a "man of the field" meaning "a worldly man." We even find that in the way he spent his time, as a hunter. Ya'aqov is then contrasted with Esau, and is called a "complete man, living in tents." In Hebrew, more often than not, when words and phrases are contrasted or paralleled, they are connected in theme. So then "man of the field" is paralleled with a man "living in tents." Indeed, if one is outside all the time, what is the opposite of that? One that is inside all the time. Many read that Ya'aqov lived in tents, and they see that as lazy, while Esau was out in the fields. But again according to Rabbinical accounts, Ya'aqov dwelled in tents because he was learning. Either way, we know that if Esau was worldly, and Ya'aqov was opposite of that, then he was NOT worldly, which is why the text also calls him "complete" here as well. Most translations say "peaceful" or "plain." "Complete" is definitely the better of these translations as we find the word used (tam) to mean just that: complete.
29 When Ya'aqov had cooked stew, Esau came in from the field and he was famished; 30 and Esau said to Ya'aqov, "Please let me have a swallow of that red stuff there, for I am famished." Therefore his name was called Edom. 31 But Ya'aqov said, "Sell your birthright to me this day." 32 Esau said, "Behold, I am about to die; so of what use then is the birthright to me?" 33 And Ya'aqov said, "Swear to me this day"; so he swore to him, and sold his birthright to Ya'aqov. 34 Then Ya'aqov gave Esau bread and lentil stew; and he ate and drank, and rose and went on his way. Thus Esau despised his birthright. – Genesis 25:29-34 (SQV)
We won't spend much time here, other than to examine something really quickly. It says that Esau "came in from the field" and thought he was about to die. In fact, he was so sure of it, that he didn't even care about his birthright. What would cause someone to be so hungry that they would seriously think they were going to die? Scripture doesn't explicitly say. However, the Book of Jasher (Sefer ha'Yashar) says that Esau had just gone out and, being the mighty hunter that he was, killed Nimrod. It says that after killing Nimrod and running from Nimrod's soldiers, he finally made it home and was hungry, and figured that the soldiers of Nimrod would find him and slay him. So he thought (and I'm paraphrasing here), "Well, I'm going to die anyway. Why die hungry?" Now as I said, Scripture doesn't say that, but if you believe the Book of Jasher, then that is definitely a possibility.
We'll skip chapter 26, since it doesn't really lend to our study here.
1 Now it came about, when Yitschaq was old and his eyes were too dim to see, that he called his older son Esau and said to him, "My son." And he said to him, "Here I am." 2 Yitschaq said, "Behold now, I am old and I do not know the day of my death. 3 Now then, please take your gear, your quiver and your bow, and go out to the field and hunt game for me; 4 and prepare a savory dish for me such as I love, and bring it to me that I may eat, so that my being may bless you before I die."
5 Rivqah was listening while Yitschaq spoke to his son Esau. So when Esau went to the field to hunt for game to bring home, 6 Rivqah said to her son Ya'aqov, "Behold, I heard your father speak to your brother Esau, saying, 7 'Bring me some game and prepare a savory dish for me, that I may eat, and bless you in the presence of YHWH before my death.' 8 Now therefore, my son, listen to me as I command you. 9 Go now to the flock and bring me two choice young goats from there, that I may prepare them as a savory dish for your father, such as he loves. 10 Then you shall bring it to your father, that he may eat, so that he may bless you before his death." 11 Ya'aqov answered his mother Rivqah, "Behold, Esau my brother is a hairy man and I am a smooth man. 12 Perhaps my father will feel me, then I will be as a deceiver in his sight, and I will bring upon myself a curse and not a blessing." 13 But his mother said to him, "Your curse be on me, my son; only obey my voice, and go, get them for me." 14 So he went and got them, and brought them to his mother; and his mother made savory food such as his father loved. 15 Then Rivqah took the best garments of Esau her elder son, which were with her in the house, and put them on Ya'aqov her younger son. 16 And she put the skins of the young goats on his hands and on the smooth part of his neck. 17 She also gave the savory food and the bread, which she had made, to her son Ya'aqov.
18 Then he came to his father and said, "My father." And he said, "Here I am. Who are you, my son?" 19 Ya'aqov said to his father, "I am Esau your firstborn; I have done as you told me. Get up, please, sit and eat of my game, that you may bless me." 20 Yitschaq said to his son, "How is it that you have it so quickly, my son?" And he said, "Because YHWH your Elohim caused it to happen to me." 21 Then Yitschaq said to Ya'aqov, "Please come close, that I may feel you, my son, whether you are really my son Esau or not." 22 So Ya'aqov came close to Yitschaq his father, and he felt him and said, "The voice is the voice of Ya'aqov, but the hands are the hands of Esau." 23 He did not recognize him, because his hands were hairy like his brother Esau's hands; so he blessed him. 24 And he said, "Are you really my son Esau?" And he said, "I am." 25 So he said, "Bring it to me, and I will eat of my son's game, that I may bless you." And he brought it to him, and he ate; he also brought him wine and he drank. 26 Then his father Yitschaq said to him, "Please come close and kiss me, my son."
27 So he came close and kissed him; and when he smelled the smell of his garments, he blessed him and said, "See, the smell of my son is like the smell of a field which YHWH has blessed; 28 Now may Elohim give you of the dew of the heavens, and of the fatness of the earth, and an abundance of grain and new wine; 29 May peoples serve you, and nations bow down to you; be master of your brothers, and may your mother's sons bow down to you. Cursed be those who curse you, and blessed be those who bless you." – Genesis 27:1-29 (SQV)
Most of us know this story pretty well, so we'll move on.
30 Now it came about, as soon as Yitschaq had finished blessing Ya'aqov, and Ya'aqov had hardly gone out from the presence of Yitschaq his father, that Esau his brother came in from his hunting. 31 Then he also made savory food, and brought it to his father; and he said to his father, "Let my father arise and eat of his son's game, that you may bless me." 32 Yitschaq his father said to him, "Who are you?" And he said, "I am your son, your firstborn, Esau." 33 Then Yitschaq trembled violently, and said, "Who was he then that hunted game and brought it to me, so that I ate of all of it before you came, and blessed him? Yes, and he shall be blessed." 34 When Esau heard the words of his father, he cried out with an exceedingly great and bitter cry, and said to his father, "Bless me, even me also, O my father!" 35 And he said, "Your brother came deceitfully and has taken away your blessing." 36 Then he said, "Is he not rightly named Ya'aqov, for he has supplanted me these two times? He took away my birthright, and behold, now he has taken away my blessing." And he said, "Have you not reserved a blessing for me?" 37 But Yitschaq replied to Esau, "Behold, I have made him your master, and all his relatives I have given to him as servants; and with grain and new wine I have sustained him. Now as for you then, what can I do, my son?" 38 Esau said to his father, "Do you have only one blessing, my father? Bless me, even me also, O my father." So Esau lifted his voice and wept.
39 Then Yitschaq his father answered and said to him, "Behold, away from the fertility of the earth shall be your dwelling, and away from the dew of the heavens from above. 40 By your sword you shall live, and your brother you shall serve; but it shall come about when you become restless, that you will break his yoke from your neck."
41 So Esau bore a grudge against Ya'aqov because of the blessing with which his father had blessed him; and Esau said in his heart, "The days of mourning for my father are near; then I will kill my brother Ya'aqov." – Genesis 27:30-41 (SQV)
Now here is where we arrive. This is why, I believe, YHWH said He hated Esau. Because Esau became all the things that YHWH hates, all at once. Consider the following:
16 There are six things which YHWH hates; yes, seven which are an abomination to Him:
17 haughty eyes, a lying tongue, hands that shed innocent blood;
18 a heart that devises plans of vain exertion, feet that are swift in running to evil,
19 a false witness who utters lies, and he who sends discord among brothers. - Proverbs 6:16-19
This does not mean that YHWH hates only 6 things. Rather, it means He hates 7 things, but the 7th is particularly an abomination.
First, we have haughty eyes. Some translations say "proud look" but literally that is not the case. The Hebrew phrase here is enayim ramowt translated literally as "eyes exalted." That is, the look that says "I'm better than you, I am exalted, I am 'above' you" and so on. Esau exalted himself above his brother, thinking that he deserved the blessing and not Ya'aqov. Esau also (as we find in Genesis 26:34-35) had no regard for the wishes of his parents, when he took foreign wives that brought grief to his parents.
Second, we have a lying tongue. Literally, this is lashon shaqer in Hebrew, meaning "tongue of falsehood." Esau said in verse 36 that Ya'aqov "took away" his birthright, but we know that is false. Ya'aqov did not take it away. Rather, Esau sold his birthright. So in his anger, he lied about how the transaction took place, thus he had a "tongue of falsehood."
Third, we have hands that shed innocent blood. In Hebrew this is v'yadayim sofekowt dam naqi or "and hands shed blood innocent." Again, we can debate whether or not Esau had killed men before, but the fact remains that his statement in verse 41 shows that he was not only capable, but also ready and willing to kill his brother, who had done nothing worthy of death.
Fourth, we have a heart that devises plans of vain exertion. Most translations say "wicked schemes" but a literal rendering in Hebrew is lev choresh machshevowt aven or "heart devises plans of vain exertion." The word aven (as noted in the Explanatory notes of the Shem Qadosh Version of Scripture) means literally "to exert effort and work for nothing." So in this, Esau planned work (to kill his brother) that would bring about nothing (both because he never went through with it, and because even if he did it would not be profitable).
Fifth, we have feet that are swift in running to evil. In Hebrew it is rag'layim m'maharowt l'ruts 'rah or "feet be swift from running to evil." Esau did not stop to think he had brought this on himself, or that he did not deserve the blessing, or even that it was his own fault for selling his birthright. Rather, the first thought he had was to kill his brother. He was brash, and in his anger was quick to run to evil.
Sixth, we have a false witness who speaks lies. In Hebrew it is y'piach k'zabim ed shaqer or "speaks lies a false witness." Again, Esau lied when he said that Ya'aqov "took away"
his birthright. This may seem identical to the "lying tongue" statement above, but it goes even further. Yes, Esau lied. However, more than that, he was a false witness. There are only two individuals mentioned being present when he sold his birthright: Ya'aqov and Esau. Two witnesses to that transaction. Thus when Esau lied about the transaction, he not only lied, but became a false witness. A lie would be telling your 90-year-old grandmother that the hideous hat she's wearing "looks good" on her. Bearing false witness would be lying about an event that took place, thus causing detriment to someone.
The seventh and last one should be the most obvious here: one who sends discord among brothers. In Hebrew it is u'm'shalach m'danim ben achim or "he sends strife/discord between brothers." Esau did not seek reconciliation, nor did he seek any sort of peaceful resolution. He sought and planned only to kill Ya'aqov. Even later on when Ya'aqov meets Esau years later, this discord is still ever present, as we find that Ya'aqov feared that Esau would still kill him (see Genesis 32 & 33).
So the 7 things which YHWH hates, including the 7th which is an abomination to Him, are all embodied in Esau. Perhaps now we can see why Esau is hated by YHWH.
I am not claiming this is all there is to the story, nor am I saying these are the only reasons YHWH says He hates Esau. This issue is certainly multi-faceted, and I believe there were continuing issues with the people of Edom (Esau) even after Esau himself was gone. Edom was blessed by YHWH, and was given their own land (Mt. Seir) which the Yisraelites were not allowed to take. Yet reading through the Twelve ("Minor") prophets we find that there is a specific judgment pronounced on Edom. YHWH Himself will bring it about in His timing.
One more facet that we can examine from this is the usage of the words "hate" and "despise." We are told that YHWH "hates" Esau, and also that Esau "despised" his birthright. To the modern mind, these words are the synonymous. Yet in Hebrew, they are quite different. The word in Malachi 1:3 is sanei meaning literally, "to hate" or "to find odious." That is, to hate something as it is found entirely offensive. Yet the word in Genesis 25:34 is bazah which means "to despise, to have contempt for" or perhaps more literally, "to have no use for." So YHWH truly hated Esau, though Esau "had no use" for his birthright. Seeing how the Hebrew culture directly ties the firstborn status to the blessing as well as the family priesthood (Exo. 13), this makes sense as well. Esau cared nothing for the responsibility that came with being the firstborn, he only wanted to be a "man of the field." Thus, he "had no use" for his birthright, and did not desire it at all until he realized that he missed his blessing. His concern was for the physical wealth that he desired as an inheritance.
So what can we personally glean from this? It should serve as a stern reminder that our behavior DOES matter. YHWH does not speak one single word that does not matter. When He says He hates something, we should make a note on how NOT to emulate that. With Esau, we find a real-life example (though albeit an extreme one) of what NOT to do. The Paul said in 1 Corinthians 10 that what happened to ancient Yisrael, happened as an example to us. Some examples show us what to do, and some show us what NOT to do. In this particular example, let us be our "brother's keeper" and not our brother's enemy as Esau was.
We can also take to heart the fact that what YHWH gave Esau (the birthright), Esau had no use for, and regarded little. On account of that, with YHWH being Just and Right, we find that He, too, found Esau of "no use." So what YHWH has given you, take to heart, and guard it. To whom much is given, MUCH will be required.
I pray this study has blessed you.
Be Berean. Shalom.
 Waugman, Elisabeth Pearson. What's in a Name? Psychology Today. 2011.
 Wikipedia. Fontanelle. https://en.wikipedia.org/wiki/Fontanelle. 2016.