Immediately Malachi employs his conversational style: a charge from the Lord, the people’s question challenging that charge, and the Lord’s answer to their challenge. In some sections the interchange goes back and forth more than once, but in each case the interchange between God and the people provides an opportunity for the Lord to expand on his first statement.
We could apply that to ourselves. ‘In what way has God loved us’, says the church. Well, you are here; you're the only empire in the world, the church of Jesus Christ, that is represented all over the world, and has been for generations, and still is, with believing worshippers everywhere. This is unprecedented. This is unique. Christ said the gates of hell would not prevail against the church, and here we are. Have we not abundant evidence of the goodness of God and the power of Christ down the centuries?
We could apply to ourselves as individual Christians. We are still here, and we are still worshipping, and yet, you and I, we have failed many, many times, but God has upheld us and restored us times without number, and blessed us and drawn us back. But here it applies to the people, the Jews of that time. God says in effect: ‘I have loved you, but’ – the implication is – ‘you haven’t loved me.’ ‘How, in what way, have we shown lack of love?’, we reply. God answers, ‘You are not aware of your calling and your privileges and your preservation. Others who put forth much more effort have disappeared, and you have been preserved.’
In Romans 9:13 Paul uses this text from Malachi to prove the doctrine of election. God exercised a choice in the case of the two brothers as Genesis 25:22-23 tells us. The doctrine of election is about individuals not about groups of people, yet Malachi uses the names of two individual sons to represent the two different nations that came from them, and points to God’s dealings with those two nations as evidence of his determination to love Israel and not Edom. How do we explain these words being used to speak of both individuals and nations? The Jews as a nation represented the church of God. The true church is made up of those only who are loved by God from all eternity, his chosen people. Israel as a nation represented that people, but only a remnant of them really knew the Lord. Nevertheless, for a limited period, in Old Testament times, God dealt with the entire nation of Israel – believers and unbelievers – as if they were the people of God. But his blessings on them and his judgments upon them took place in the physical realm, and at the level of their earthly affairs. God could bless them at this level and still distinguish between believers and unbelievers among them. Only a remnant of Israel was ever saved. And yet God favoured the nation as a whole, as a picture of what he would in future do for his true people, those who are born again. At that time, through Malachi, the Lord points to the national blessings Israel had received, and at this level they had strong cause to be encouraged. But the election of God which brings us into his kingdom operates at the individual level, and this is what Paul quotes Malachi to prove. That election operated in every generation, and is Paul’s explanation for how so many Israelites failed to believe. Jacob was loved, not Esau; the promised seed [Christ] was through Isaac, not Ishmael; from Israel only a remnant was called.