Isaac favored Esau. Rebekah favored Jacob. Isaac and Rebekah didn’t love both of their sons equally? Rebekah told Jacob to put on Esau’s clothes so that he can receive Esau’s blessings from his father. Why didn’t God stop Jacob?
It is fairly obvious that Isaac and Rebekah did not love their sons equally. This is nothing new though, Noah clearly showed favor to Japheth and Shem over Ham, Abraham showed favor to Isaac over Ishmael, and Jacob infamously showed favor to Joseph over all his other brothers. Remember that these men and women were not perfect people, they were sinful humans who had wills of their own.
Rebekah even stooped so low as to deceive her husband so to advance her own will and see that Jacob would get the blessing from Isaac. God did not stop Jacob for a couple reasons. First of all, we are not puppets and God is not a puppet master, God allows us to make decisions that are deceitful and evil, but he also allows us to make decisions that are righteous and ultimately glorifying to him (learn more about God’s will and our will here). Secondly, God can accomplish his will despite our deception and evil. Esau may have deserved the blessing by birth right, but he was also an impulsive glutton who had already traded away his birth right to Jacob for some soup (see Genesis 25:29-34). God had his reasons for allowing this deceit to take place, and ultimately God’s will would be done even in the midst of it. As you continue to read the story, you see the way that God establishes his people through the line of Jacob. And as Jacob’s son Joseph says to his brothers at the end of Genesis, “what you meant for evil God meant for good,” this is also the case with Jacob and many others in scripture.