If God has the authority to make some for glory and others for destruction (Rom. 9:22), how can John 3:16 say He desires to save the whole world?

A mistaken premise can lead to confusing conclusions. Let’s rethink this question. First, Romans 9:2–23 teaches that God has “mercy on whom he wants to have mercy” (v. 18, the predestination of believers). However, when speaking of “objects of his wrath—prepared for destruction” (v. 22) the text never says who prepared them. The verb “prepared” may mean that the vessels were prepared for destruction by someone else. Or it may mean that the vessels of wrath prepared themselves for destruction. Either way, God is not the One who prepared them.

Second, John 3:16 says God loved the world not that He desires to save the whole world. In 2 Peter 3:9 it says that God is patient, “not wanting anyone to perish, but everyone to come to repentance.” It is God’s desire that we repent and receive mercy but not His decree. He longs for us to be saved but He has not predestined all for universal salvation.