The concept of God hating Esau seems somewhat alien to us in our modern culture. It contradicts everything we think we know about God. Is God not love? Does He not love the world? Indeed, does He not want all men to be saved? And yet, here it seems pretty clear cut: God hated Esau. The problem is, it seems clear cut because the verse has actually been cleanly cut.
The first thing we need to do here is to discard our cultural views. Although it is certainly true, indisputably so, that God does not want anyone to perish, that He wants all men saved, that He takes no pleasure in the death of the wicked, and that He loves the world, it is entirely possible to take that to an extreme. The idea of God we often have in our heads is a cuddle merchant. He stops just short of being a magical genie (and heck, some people don't even stop there), having not one shred of hatred in Him. But my brethren, have you ever heard of Hell?
In His love, God provided a way for us to avoid Hell, but I want you to imagine for a moment, what if He didn't? What if God considered Himself above our pitiful, human existence, and decided that, since He is not really obligated to save anyone, He might as well not go through that? Dear brethren, salvation is so far beyond extra that we can't even comprehend it. The very offer is the picture of His love. But had He not provided that, we would all be in Hell. Many people will go there anyway.
And what is Hell? I can promise you this: It is not a thing beyond God's control. Indeed, it is very much within His control. It is actually His wrath against sin. His vengeance against those who would dare oppose Him. It shows just how much He hates sin. And if the sinner will not be separated from it? Well, the Bible tells us that God is angry with the wicked every day (Psalm 7:11). God's justice ultimately means that He must hate the impenitent sinner. Therefore, it is entirely possible for Him to hate an individual, even one whom He otherwise loved, especially as He knows who will and will not be saved.
But this is not actually what we are dealing with here. See, notice first how Paul is actually quoting a previous scripture. "As it is written." Thus, in order to understand the context of Romans 9:13, we must turn to...
Malachi 1:2-5: "“I have loved you,” says the Lord. “Yet you say, ‘In what way have You loved us?’ Was not Esau Jacob’s brother?” Says the Lord. “Yet Jacob I have loved; But Esau I have hated, And laid waste his mountains and his heritage For the jackals of the wilderness.” Even though Edom has said, “We have been impoverished, But we will return and build the desolate places,” Thus says the Lord of hosts: “They may build, but I will throw down; They shall be called the Territory of Wickedness, And the people against whom the Lord will have indignation forever. Your eyes shall see, And you shall say, ‘The Lord is magnified beyond the border of Israel.’"
And so we see that actually, God is not talking about His love for the two literal brothers. Rather, He is using them as a symbol of the nations to whom they gave rise. Jacob gave rise to the nation of Israel, the nation to whom God committed His oracles, and ultimately from whom the Messiah should rise. Esau gave rise to the nation of Edom, a rebellious nation God would use not for honour, but for dishonour. We don't know the fate of Esau himself. Personally, it looks to me like he eventually repented and reconciled with his brother, ultimately receiving many blessings from God. He may well have been saved. Do not take my word for that. Rather, study the scriptures, and see if I am in error. That is not even the point of today's article. Whatever happened with Esau, on Earth or in eternity, Malachi 1 is obviously not discussing Esau as an individual. Therefore, Romans 9:13, which uses Malachi 1 as a foundation, also cannot be discussing Him as a person.
And indeed, the rest of Romans 9 bears this out. First, verse 13 is a continuation of the thought begun in verse 6. Here, Paul distinguishes between children in the flesh, and children in the seed. Jacob is not the only patriarch in view here. Isaac also, and Abraham before him. The point is, it doesn't matter if you are descended from Abraham if you are not descended also from Isaac, for are the Ishmaelites not also descended from Abraham? And if from Isaac, that's still not enough, for aren't the Edomites also descended from Isaac? And so Paul distinguishes between children in the flesh and children of the promise. "...they are not all Israel who are of Israel" (v6).
And of course, Paul does not stop at discussing the distinction between "Jacob" and "Esau". He continues to remind us that God will have mercy on whom He will have mercy, and compassion on whom He will have compassion. Then we move on to Pharaoh. Paul reminds us that scripture says to Pharaoh "For this very purpose I have raised you up, that I may show My power in you, and that My name may be declared in all the earth." And from this, God is said again to have mercy on whom He will have mercy, but also "whom He wills, He hardens."
So here, we actually are talking about an individual, namely Pharaoh, but even he represents his nation. Furthermore, we actually see that there was a purpose to this. It wasn't just "I really don't like this Pharaoh guy, so I'm going to really mess up his day." Rather, God took an already sinful person, and set him up as a ruler so God could display His glory through him.
From here, Paul force feeds us some humble pie. He foresees the natural objection to this. If God ordains these things, how can He find fault? Indeed, even to this day, many atheists and other unbelievers love to pick up on the fact that God hardened Pharaoh's heart, and they ask how it was Pharaoh's fault? Paul's response: "who are you to reply against God? Will the thing formed say to him who formed it, “Why have you made me like this?” Does not the potter have power over the clay, from the same lump to make one vessel for honor and another for dishonor?"
If God wants to raise up a nation, He has that right. If God wants to bring it down, even completely destroy it, that's entirely His business. Just as my mug cannot object when I use it as a flower pot, nations cannot complain when God punishes their sins. Even Sodom, though they would have repented had the Lord done miracles among them (Matthew 11:23), has no case against God though He instead burned them to the ground.
From this, Paul continues to say "What if God, wanting to show His wrath and to make His power known, endured with much longsuffering the vessels of wrath prepared for destruction, and that He might make known the riches of His glory on the vessels of mercy, which He had prepared beforehand for glory, even us whom He called, not of the Jews only, but also of the Gentiles?"
This continues to answer the same question on a grander scale. We may ask why God hardened Pharaoh's heart, but that is nothing compared to the question of why God, knowing many would be destroyed, still chose to create them? And so Paul poses the hypothetical: What if God just wants to show us His wrath and power, as well as the riches of His glory? Think back to what I said before about how salvation is extra. God could so easily have left us to destruction. He loses literally nothing when a sinner is lost. We do not deserve salvation, God does not owe us salvation, and yet He gives it to us anyway. And so we, as vessels of mercy, fully understand where we stand with God. We see His power, we see His sovereignty, we see His love, all because though He takes no pleasure in enforcing justice, He nevertheless does so. Yet not against us. Through His own Son's death, God has mercy on us. So what if that's what God is going for? Do we have the right to object? Nope.
And as we read on in Romans 9, we see that all of this has one simple point: It explains Israel's present condition with regard to Jesus. They believe they are special because of Abraham, and yet they are wrong because they do not have Christ. There is the faithful remnant, preserved by grace of God, but most of Israel has rejected Christ. This is ordained by God, just as any other thing. Just as the rebellion of the Edomites was ordained, just as Pharaoh's hardened heart was ordained, so also was Israel's rejection of Christ. It's all in His plan to save both Jew and Gentile alike, showing His glory through both the saved and the unsaved. Thus, the TL;DR of Romans 9 isn't that God discriminates or shows favouritism, but that God is sovereign, that God's thoughts are higher than our thoughts, and that we should consider our place before Him. As with the entire Bible, God's glory is in view here.